The first list of epiphytic diatom species on the seagrass Thalassia testudinum from the Yalahau lagoon area in the Mexican Caribbean is given. One hundred and seven diatom taxa living on T. testudinum were identified including species and varieties. Nine taxa are new records for Mexico. The Bacillariophyceae with 87 taxa were the most diverse group. The most abundant taxa were: Cocconeis lineata, Mastogloia crucicula var. crucicula, Cocconeis thalassiana, Cocconeis scutellum var. scutellum and Mastogloia ovata, representing approximately 75% of the total valve count (N = 1527). Yalahau lagoon samples from site 1 yielded a high number of rare taxa. Species richness (S), diversity (H′, 1-λ) and equitability (J′) for the lagoon were lower than for Cabo Catoche (site 2). Based on presence/absence of species, the measured similarity (60%) suggests that the diatom assemblages growing on T. testudinum in the two localities are different.