The evaluation of geographic distribution of Pyropia along the Gulf of California, Mexico, was realized using molecular data from two loci, the plastid rbcL gene and the partial 18S ribosomal DNA (rDNA), in conjunction with morphological observations. Dawson described two endemic species for the genus Pyropia (Pyropia hollenbergii and Pyropia pendula) in the Gulf of California based on taxonomic characteristics. In this study, we collected 130 samples from 13 locations from February 1998 to April 2008. Samples showed similar morphologies and growth habits and share a very similar type descriptions and habitat records. Using morphological and anatomical characteristics, we identify individuals as P. hollenbergii and P. pendula. However, using the molecular data, we identified five identities, which we have classified as P. hollenbergii, P. pendula, Pyropia sp. Gulf of California I (GCI), Pyropia sp. GCII, and Pyropia sp. GCIII. Phylogenetic trees based on partial 18S rDNA and rbcL sequence data showed a deep division in the genus that is not obviously correlated with existing morphological characteristics and indicate that representatives of the Gulf of California flora have undergone long reproductive isolation.