A rapidly increasing stray animal population in Bangkok has caused concern regarding transmission of vector-borne and zoonotic diseases. The purpose of this study was to determine if stray animals in Bangkok are a potential reservoir of Hepatozoon, a genus of tick-borne parasites that has received little attention in Thailand. Blood samples were collected from stray companion animals near monasteries in 42 Bangkok metropolitan districts. Both dogs and cats were sampled from 26 districts, dogs alone from 4 districts and cats alone from 12 districts. Samples were collected from a total of 308 dogs and 300 cats. Light microscopy and an 18 S rRNA gene-based PCR assay were used to test these samples for evidence of Hepatozoon infection. Gamonts were observed in blood smears for 2.6% of dogs and 0.7% of cats by microscopy. The PCR assay detected Hepatozoon in buffy coats from 11.4% of dogs and 32.3% of cats tested. The prevalence of infection was the same between male and female dogs or cats, and PCR-positive dogs and cats were found in 36.6% and 36.8% of the districts surveyed, respectively. There was an association between the percentages of PCR-positive dogs and cats in districts where both host species were sampled. Sequences of representative amplicons were closest to those reported for H. canis. These results represent the first molecular confirmation that H. canis is indigenous to Thailand. The unexpectedly high prevalence of Hepatozoon among stray cats indicates that their role in the epizootiology of hepatozoonosis should be investigated.