Hemoplasmosis caused by Mycoplasma spp. have been associated with major economic losses in the global dairy production. Hemoplasma studies in the Philippines are limited despite its potential impact. This study mainly aimed to detect the presence of hemoplasma species in dairy water buffaloes and cattle and know their ectoparasite biodiversity in Bohol, Philippines. Detection of Mycoplasma spp. was performed using peripheral blood smear examination (PBSE) and standard PCR using whole blood samples collected from 100 dairy water buffaloes and 40 dairy cattle. Available records on the average annual, monthly and daily milk production were compared between PCR-positive and PCR-negative animals. Ectoparasites were manually collected and identified. While PBSE results were all negative, PCR testing showed that 80% (80 water buffaloes and 32 cattle) were positive for Mycoplasma spp. On the other hand, a total of 1436 ectoparasites were collected (609 Haematopinus and 827 Rhipicephalus spp.). DNA sequencing revealed that obtained sequences (193 bp) from 7 animals were 99.5 to 100% similar to registered Mycoplasma wenyonii sequences. The study reports the first molecular characterization of M. wenyonii in the Philippines and probably the first detection in dairy water buffaloes in Southeast Asia.