Abstract: Cocoa farming is affected by many fungal diseases and frosty pod rot is one of the biggest constraints of cocoa cultivation in Latin America cocoa growing countries. Three Moniliophthora roreri strains have been isolated from frosty pod rot diseased cocoa tree (Theobroma cacao) in Tabasco, Mexico. The strains were identified by morphological analysis and by sequencing the internal transcribed spacers 1 and 2. The microscopic and macroscopic morphological characteristics observed are similar to those reported in the literature for those species. The phylogenetic analysis of the M. roreri sequences formed three groups supported by high bootstrap values and the sequences of the isolates clustered close to the sequences of strains previously isolated from T. cacao in Peru and Mexico. The alignment of ITS1-5.8s-ITS2 sequences of M. roreri strains revealed for ITS1 and ITS2 four regions with interspecies divergence (80, 84-91, 110 and 130) and six (395, 444, 459, 539, 570 and 585), respectively. In conclusion, the identification of M. roreri cocoa strains by ITSs sequences confirmed the identification by morphological methods and provides information on the variability in comparison with M. roreri strains of South and Central America. Besides this, the identification could be important for developing strategies for its prevention and control.