A survey for Infectious Hypodermal and Haematopoietic Necrosis Virus (IHHNV) and White Spot Syndrome Virus (WSSV) was performed during two catching seasons of native shrimps in the Yucatan Coast in the Gulf of Mexico. The mtDNA COI barcode identified two endemic species; the southern pink shrimp Penaeus notialis (Pérez Fantante, 1967) and the northern pink shrimp Penaeus brasiliensis (Latreille, 1987) (previously described as Farfantepenaeus brasiliensis). The prevalence of IHHNV was of 18.18% in 2016, and of 8.57% in 2017. All organisms tested negative for WSSV. This is the first identification of wild shrimps in the state of Yucatan Mexico by mtDNA COI barcode as well as the first identification of IHHNV in such species. The presence of IHHNV in wild shrimps populations has a potential of persisting in the coast of Yucatan with putative detrimental effect on local fisheries because once established in natural waters and hosts; such pathogens are almost impossible to eradicate.