Vanilla claviculata (W. Wright) Sw. and V. barbellata Rchb.f. grow sympatrically in the southwestern part of herto Rico. At three localities in the range of the two species, individuals with flowers that appeared different from previously known species were found. To test whether these were hybrids between V. claviculata and V. barbellata, 11 morphological floral characters were recorded at seven populations and allozyme profiles of the three taxa compared. Principal component analysis on the morphological characters gave three distinct groups with minor overlaps. The first component axis reflects variation in overall size of the flowers, while the second component reflects variation in the size of the distal aperture of the labellum. Allozyme data revealed that the putative hybrids have a significant surplus of heterozygotes (FIS= − 0.65) as expected in a F1 generation. Both data sets support the hypothesis that the individuals are hybrids, which is further augmented by interspecific pollination experiments between the putative parental species. This is the first case of natural hybridization reported in the genus Vanilla.