The search for exotic pathogens related to the outbreaks and in surveillance samplings of the Mexican oyster farms, is a recent activity achieved by academic institutions and state committees for Aquatic Animal Health, with remarkable results. In samples of Crassostrea gigas collected through December 2009, January 2010 and November 2010, and of C. corteziensis in September 2011, the protozoan Marteilia refringens was detected for the first time in the Gulf of California. The carrier oysters were from cultures without abnormal mortality rates, whereby, the use of histology, in situ hybridization and transmission electron microscopy studies are necessary to determine if M. refringens has become established in the Gulf of California oyster cultures. Detection of M. refringens is of great concern to the global oyster farming industry.