The mountains of the southeast Iberian Peninsula harbor several narrowly endemic species belonging to Narcissus section Pseudonarcissi (N. alcaracensis, N. bugei, N. enemeritoi, N. longispathus, N. nevadensis, N. segurensis, and N. yepesii) that are protected by regional Spanish laws. Most of these trumpet daffodils show a very similar overall morphology, and the correct identification of species is difficult unless the geographical origins of the accessions are known. ISSR (Inter-Simple Sequence Repeat) and nuclear ribosomal ITS sequences were used to assess patterns of genetic discontinuities present among the members of this section from southeast Spain. Species-specific ISSR bands were found in N. bugei, N. longispathus and N. nevadensis, but were absent in the other species. The multivariate ordination of the 288 ISSR-genotyped accessions showed that only N. longispathus and N. bugei were clearly differentiated, while the other species formed an unresolved group. ITS sequences of N. bugei were highly divergent from those retrieved from the remaining species, which were placed in a single largely unresolved clade in phylogenetic analysis. In conclusion, ISSR and ITS markers support the taxonomic distinction of N. bugei and N. longispathus. However, N. alcaracensis, N. segurensis, N. yepesii, N. enemeritoi, and N. nevadensis could be merged within a single species (N. nevadensis for nomenclatural priority).