Infectious diseases have been a major limiting factor for large scale production of oyster farming. Several factors have contributed to the emergence and spread of infectious diseases in all cultivation sites around the world. Therefore, the prevention and control of diseases has become a priority for the sustainability of global aquaculture. Crassostrea corteziensis is a native species that contributes to the Mexican Pacific oyster production and used in this study to assess seasonal simultaneous infective events between distant areas in the Gulf of California. The results of the molecular analysis showed a higher prevalence of Perkinsus marinus in the north area and Marteilia refringens in the south. OsHV-1 was only present in summer and autumn with low prevalence in the two areas. The histological analysis of the PCR-positive organisms presented alterations characteristic of infections. The presence of M. refringens in a new location on the Gulf of California suggests that this pathogen is already well established in the area and the dual presence of pathogens in C. corteziensis is reported for the first time.