A novel Caribbean species Albula sp. cf. vulpes in the family Albulidae (bonefishes) was diagnosed through genetic and morphometric study. Phylogenies derived from 16S rRNA sequences revealed deeply separated lineages among Caribbean bonefishes. Mitochondrial DNA sequence divergences indicated a separation between 3·0 and 5·2 million years before present (b.p.). Cytochrome b phylogenies further supported the classification of A. sp. cf. vulpes as a novel albulid. Morphological variability revealed several differences between A. sp. cf. vulpes and other Caribbean species. A microsatellite library was developed to discern hybridization rates among the species. Microsatellite analyses revealed low levels of hybridization between some members in the complex. One instance of backcrossing was found between A. vulpes×A. sp. B and a pure A. sp. B, indicating that hybrids may have reduced fitness or may be reproductively isolated due to temporal–spatial spawning habitat differences.