Filariasis is emerging as a public health concern in tropical and subtropical areas. Filariasis is an endemic problem commonly found in southeast Asian countries. Using the PCR-restriction fragment length polymorphism (PCR-RFLP) of the ITS1 region with Vsp I, the overall prevalence rates of Dirofilaria immitis (12.2% (41/337); 95% confidence interval: 9.1–16.1%) and Brugia pahangi (8.3% (28/337); 95% confidence interval: 5.8–11.8%) were determined based on 337 free-roaming community dogs from 20 districts in Northern Thailand. Microfilaremia was found in only 6.2% of dogs (21/337). Co-infection with D. immitis and B. pahangi was observed in two dogs. Of the 215 blood samples examined using a Canine Heartworm Ag Kit, only 3.72% (eight dogs) were D. immitis antigen positive. Among these eight, six dogs had occult D. immitis infections. In terms of geographic distribution, we found the abundance of D. immitis and B. pahangi in the central areas at altitudes less than 400 m to be 12.1% and 10.3%, respectively. In contrast, at higher altitudes between 400 and 800 m, a significantly higher number of B. pahangi compared with D. immitis infected individuals were observed at 14.29% and 4.1%, respectively. In conclusion, D. immitis and B. pahangi were the most common filarial infections found in community dogs in Northern Thailand. Dogs might be an important reservoir of B. pahangi in that region. Increasing awareness and concern and including proper deworming programs for community dogs should be endorsed to reduce the transmission risk. Additionally, the population dynamics of the mosquito vector of B. pahangi across altitudinal gradients deserved further investigation.