Oysters cultured in the Manila Bay, specifically in Cavite City; Naic, Cavite; and Obando, Bulacan, were surveyed for the occurrence of Perkinsus sp. for three months from June to August 2012. Ray’s fluid thioglycollate medium (RFTM) revealed the presence of Perkinsus sp. hypnospores in oyster tissues. Based from the hypnospores present, the infection rate was recorded highest in Obando, Bulacan, with 79.4%, followed by Naic, Cavite, with 66.1% and Cavite City with 62.8% as the lowest. Light infection intensity was likewise recorded highest in Obando, Bulacan, with 18.93, followed by Naic, Cavite, with 12.86 and Cavite City with 12.56 as the lowest in which no significant differences occurred across sites. However, a decreasing pattern in the intensity of infection was observed from June to July 2012, and an increase was observed in the month of August 2012, which revealed significant differences across the collection period, specifically during July 2012 and the first collection in August 2012. Furthermore, histological sections were made to confirm the RFTM for the occurrence of the parasite and its potential damage to the host tissue. Oyster hemocytes were likewise observed along with Perkinsus sp. Circular damage in the mantle was evident. In comparison with the usual size of Perkinsus sp. which is ~1 μm, the observed smaller size of the trophozoite stage is indicative of a species only endemic in the country.