Fernández de Castro, A.; Rozas, V.; Fuertes-Aguilar, J.; Moreno Saiz, J.C. 2020. Demographic and dendrochronological evidence reveals highly endangered status of a paleoendemic woody mallow from the Canary Islands. Biodiversity and Conservation 29:469-485. 

Villa-Machío, I.; Fernández de Castro, A.G.; Fuertes-Aguilar, J.; Nieto Feliner, G. 2020. Colonization history of the Canary Islands endemic Lavatera acerifolia, (Malvaceae) unveiled with genotyping-by-sequencing data and niche modelling. Journal of Biogeography 47(4):993-1005. 

Cetlová, V.; Fuertes-Aguilar, J.; Iudova, S.; Španiel, S. 2019. Overlooked morphological variation and a proposal for a new taxonomic circumscription of Alyssum simplex (Brassicaceae). Phytotaxa 416(2):149-166. 

Salmerón-Sánchez, E.; Fuertes-Aguilar, S.; Španiel, S.; Pérez-García, F.J.; Merlo, E.; Garrido-Becerra, J.A.; Mota, J. 2018. Plant evolution in alkaline magnesium-rich soils: A phylogenetic study of the Mediterranean genus Hormathophylla (Cruciferae: Alysseae) based on nuclear and plastid sequences. PLoS ONE 13(12):e0208307. 

Villa-Machío, I.; Fernández de Castro, A.G.; Fuertes-Aguilar, J.; Nieto Feliner, G. 2018. Out of North Africa by different routes: phylogeography and species distribution model of the western Mediterranean Lavatera maritima (Malvaceae). Botanical Journal of the Linnean Society 187(3):441-455. 

Bello, M.A.; Cubas, P.; Álvarez, I.; Sanjuanbenito, G.; Fuertes-Aguilar, J. 2017. Evolution and Expression Patterns of CYC/TB1 Genes in Anacyclus: Phylogenetic Insights for Floral Symmetry Genes in Asteraceae. Frontiers in Plant Science 8:art.589.

Fernández de Castro, A.G.; Moreno-Saiz, J.C.; Fuertes-Aguilar, J. 2017. Ornithophily for the non-specialist: Differential pollination efficiency of generalist passerines on the Macaronesian island paleoendemic Navaea phoenicea (Malvaceae). American Journal of Botany 104(10):1556-1568.

Fuertes Aguilar, J.; Villa-Machío, I. 2017. Claves moleculares de la biodiversidad vegetal. Revista de la Sociedad Española de Bioquímica y Biología Molecular 193:15-18.

Marques, I.; Fuertes Aguilar, J.; Martins-Louçao, M.A.; Moharrek, F.; Nieto Feliner, G. 2017. A three-genome five-gene comprehensive phylogeny of the bulbous genus Narcissus (Amaryllidaceae) challenges current classifications and reveals multiple hybridization events. Taxon 66(4):832-854.

Nieto Feliner, G.; Álvarez, I.; Fuertes-Aguilar, J.; Heuertz, M.; Marques, I.; Moharrek, F.; Piñeiro, R.; Riina, R.; Rosselló, J.A.; Soltis, P.S.; Villa-Machío, I. 2017. Is homoploid hybrid speciation that rare? An empiricist’s view. Heredity 118:513-516. 

Bello, M.A.; Martínez-Asperilla, A.; Fuertes-Aguilar, J. 2016. Floral development of Lavatera trimestris and Malva hispanica reveals the nature of the epicalyx in the Malva generic alliance. Botanical Journal of the Linnean Society 181:84-98.

Marques, I.; Jürgens, A.; Fuertes Aguilar, J.; Nieto Feliner, G. 2016. Convergent recruitment of new pollinators is triggered by independent hybridization events in Narcissus. New Phytologist 210(2): 731-742. 

Salmerón-Sánchez, E.; Fuertes Aguilar, J.; Spaniel, S.; Mendoza-Fernández, A.J.; Martínez-Hernández, F.; Mota, J.F. 2016. The status of Hormathophylla baetica: A new combination and lectotypification in Hormathophylla cochleata. Phytotaxa 280(1):45-54.

Bello, M.A.; Alvarez, I.; Torices, R.; Fuertes-Aguilar, J. 2013. Floral development and evolution of capitulum structure in Anacyclus (Anthemideae, Asteraceae). Annals of Botany. doi: 10.1093/aob/mcs301     

Marques, I.; Fuertes Aguilar, J.; Martins-Loução, A.; Nieto Feliner, G. 2012. Spatial-temporal patterns of flowering asynchrony and pollinator fidelity in hybridizing species of Narcissus. Evolutionary Ecology 26:1433-1450.

Marques, I.; Nieto Feliner, G.; Martins-Loução, A.; Fuertes Aguilar, J. 2012. Genome size and base composition variation in natural and experimental Narcissus hybrids. Annals of Botany 109: 257-264.

Fuertes Aguilar, J.; Gutiérrez Larena, B.; Nieto Feliner, G. 2011. Genetic and morphological diversity in Armeria (Plumbaginaceae) shaped by glacial cycles in southern Mediterranean refugia (Sierra Nevada, Spain). Anales Jard. Bot. Madrid 68: 175-197.

Marques, I.; Nieto Feliner, G.; Martins-Loução, A.; Fuertes Aguilar, J. 2011. Fitness in Narcissus hybrids: low fertility is overcome by early hybrid vigor, absence of exogenous selection and high bulb propagation. Journal of Ecology  99: 1508-1519

Escobar Garcia, P.; Schoenswetter, P.; Fuertes Aguilar, J.; Nieto Feliner, G.; Schneeweiss, G.M. 2009 Five Molecular Markers Reveal Extensive Morphological Homoplasy and Reticulate Evolution in the Malva Alliance (Malvaceae). Molecular Phylogenetics and Evolution 50 (2): 226-239.

Piñeiro, R.; Costa, A.; Fuertes Aguilar, J.; Nieto Feliner, G. 2009. Overcoming paralogy and incomplete lineage sorting to detect phylogeographic signal: a GapC study of Armeria pungens. Botany 87: 164-177.

Piñeiro, R.; Aguilar, J.F.; Munt, D.D.; Feliner, G.N. (2007). Ecology matters: Atlantic-mediterranean disjunction in the sand-dune shrub Armeria pungens (Plumbaginaceae). Molecular Ecology, 16 (10), 2155-2171.

Tate, J. A.; Fuertes Aguilar, J.; Wagstaff, S.J.; La Duke, J. C.; Bodo Slotta, T. A.; Simpson, B. B. (2005). Phylogenetic relationships within the tribe Malveae (Malvaceae, subfamily Malvoideae) as inferred from ITS sequence data. American Journal of Botany 92(4): 584 - 602.

Nieto Feliner, G.; Gutiérrez Larena, B.; Fuertes Aguilar, J. (2004). Fine scale geographical structure, intra-individual polymorphism and recombination in nuclear ribosomal internal transcribed spacers in Armeria (Plumbaginaceae). Annals of Botany 93: 189-200.

Fuertes Aguilar, J.; Nieto Feliner, G. 2003. Additive polymorphisms and reticulation in an ITS phylogeny of thrifts (Armeria, Plumbaginaceae). Molecular Phylogenetics and Evolution 28(3):430-447.

Fuertes Aguilar, J.; Fryxell, P. A.; Jansen R K. 2003. Phylogenetic relationships and classification of the Sida generic alliance (Malvaceae) based on nrDNA ITS evidence Systematic Botany 28 (2): 352-364.

Fuertes Aguilar, J.; Francisco Ortega, J.; Santos-Guerra, A.; Ray, M. F.; Jansen, R.K. 2002. Chloroplast and nuclear molecular evidence for multiple colonizations of Lavatera (Malvaceae) in the Canary Islands. Systematic Botany 27: 74-83.

Gutiérrez Larena, B.; Fuertes Aguilar, J.; Nieto Feliner, G. 2002. Glacial-induced altitudinal migrations in Armeria (Plumbaginaceae) inferred from patterns of cpDNA haplotype sharing. Molecular Ecology 11: 1965-1974.

Fuertes Aguilar, J.; Rosselló, J.A.; Nieto Feliner, G. 1999. Molecular evidence for the compilospecies model of reticulate evolution in Armeria (Plumbaginaceae). Systematic Biology 48: 735-754. 

Ojeda D.I.; Valido A.; Fernández de Castro A.G.; Ortega-Olivencia A.; Fuertes-Aguilar J.; Carvalho J.A.; Santos-Guerra A. 2016. Pollinator shifts drive petal epidermal evolution on the Macaronesian Islands bird flowered species. Biology Letters 12: 20160022.

Piñeiro, R.; Widmer, A.; Fuertes Aguilar, J.; Nieto Feliner, G. 2011. Introgression in peripheral populations and founder effects shape genetic structure of the coastal shrub Armeria pungens. Heredity 106: 228-240.

Marques, I.; Nieto Feliner, G.; Draper, D.; Martins-Loução, A.; Fuertes Aguilar, J. 2010. Unraveling cryptic reticulate relationships and the origin of orphan hybrid disjunct populations in Narcissus. Evolution 64: 2353–2368.

Piñeiro, R.; Fuertes Aguilar, J.; Menezes de Sequeira, M.; Nieto Feliner, G. (2009). Low genetic diversity in the rare Madeiran endemic Armeria maderensis (Plumbaginaceae). Folia Geobotanica 44:65–81.

Larena, B.G.; Aguilar, J.F.; Nieto Feliner, G. 2006. Dispersal across Southern Iberian refugia? Integrating RAPDs, sequence data and morphometrics in Armeria (Plumbaginaceae). Folia Geobotanica 41 (3): 305-322.

Albaladejo, R.G.; Fuertes Aguilar, J.; Aparicio, A.; Nieto Feliner, G. 2005. Contrasting nuclear-plastidial phylogenetic patterns in the recently diverged Iberian Phlomis crinita and P. lychnitis lineages (Lamiaceae). Taxon 54 (4): 987-998.

Gutiérrez Larena, B.; Fuertes Aguilar, J.; Nieto Feliner, G. 2004. Morphometric and molecular evidence for recognition of a new subspecies of Armeria filicaulis (Plumbaginaceae). Anales Jard. Bot. Madrid 61: 35-48. 

Lihová, J.; Fuertes Aguilar, J.; Marhold, K.; Nieto Feliner, G. 2004. Origin of the disjunct tetraploid Cardamine amporitana (Brassicaceae) assessed with nuclear and chloroplast DNA sequence data. American Journal of Botany 91(8): 1231–1242.

Francisco Ortega, J.; Fuertes Aguilar, J.; Kim, S.C.; Santos-Guerra, A.; Crawford,D.J.; Jansen, R.K. 2002. Phylogeny of the Macaronesian endemic Crambe section Dendrocrambe (Brassicaceae) based on internal transcribed spacer sequences ofnuclear ribosomal DNA. American Journal of Botany. 89: 1984-1990.

Nieto Feliner, G., Fuertes Aguilar, J.; Rosselló, J. A. (2002). Reticulation or divergence: the origin of a rare serpentine endemic assessed with chloroplast, nuclear and RAPD markers. Plant Systematics and Evolution 231: 19-38.

Alvarez Fernández, I.; Fuertes Aguilar, J.; Panero, J. L.; Nieto Feliner, G. 2001. A phylogenetic analysis of Doronicum (Asteraceae,Senecioneae) based on morphological, nuclear ribosomal (ITS) and chloroplast (trnL–F) evidence. Molecular Phylogenetics and Evolution 20: 41-64.

Fuertes Aguilar, J. 2001. Lacolección de láminas de Mutis del archivo de la Expedición Malaspina.In: M.P. De San Pío Aladrén & M.D.Higueras Rodríguez (coords.), La armonía natural. La naturalezaen la expedición marítima de Malaspina y Bustamante 1789-1794.Catálogo de los fondos documentalesdel Real jardín Botánico. Pp. 85-92.Real Jardín Botánico, Lunwerg y CajaMadrid. Madrid.

Nieto Feliner, G.,Fuertes Aguilar, J., Rosselló, J. A. (2001). A new species of Armeria (Plumbaginaceae) from southern Spain with molecular and morphometric evidence on its origin. Botanical Journal of the Linnean Society 135(1): 71-84.

Nieto Feliner, G.; Fuertes Aguilar, J.; Rosselló, J.A.(2001). Can extensive reticulation and concerted evolution result in a cladistically structured molecular data set? Cladistics 17(4): 301-312. 

Francisco Ortega, J.; Fuertes Aguilar, J.; Gómez-Campo, C.; Santos Guerra, A.;  Jansen. R.K. 1999. Internal Transcribed Spacer Sequence Phylogeny of Crambe L. (Brassicaceae): Molecular Data Reveal Two Old World Disjunctions. Molecular Phylogenetics and Evolution 11(3): 361-380.

Fuertes Aguilar, J.; Rosselló, J. A.; Nieto Feliner, G. 1999. Nuclear ribosomal DNA (nrDNA) concerted evolution in natural and artificial hybrids of Armeria (Plumbaginaceae). Molecular Ecology 8: 1341-1346. 

Fuertes Aguilar, J. 1998. Catálogo de los dibujos, identificación y descripción de las especies vegetales. In: La Comisión Naturalista de Löfling en la Expedición de Límites al Orinoco. Lunwerg Editores, Madrid. ISBN: 84-7782-561-0. pp: 111-173.