Background Brugia malayi is the most common cause of lymphatic filariasis (LF) in Indonesia. A zoophilic ecotype that infects both humans and animals occur in Belitung District in Indonesia. The district received five annual rounds of mass drug administration (MDA) between 2006 and 2010 and passed three transmission assessment surveys (TAS) in subsequent years. However, a survey in five villages in 2021 showed a microfilaria (Mf) prevalence of 2.1% in humans. The reappearance of B. malayi infection in humans may be due to reintroduction from animal reservoirs. The goal of this study was to determine B. malayi prevalence in potential reservoir hosts and to improve the identification of filarial Mf found in animals. Methodology/principal findings Venous blood was collected from 291 cats, 41 dogs, and 163 crab-eating macaques (Macaca fascicularis) from areas with and without human B. malayi infection. B. malayi Mf were detected by microscopy in 1.4%, 7.3% and 13.5% of the samples, respectively. The geometric mean Mf density varied from 133 Mf/mL(dogs) to 255 Mf/mL (macaques). While Brugia Mf were easily differentiated from Dirofilaria Mf by microscopy, the morphological differentiation between B. malayi and B. pahangi was not reliable. qPCR detected B. malayi DNA in blood from 4.1% of cats, 2.4% dogs, and 13.5% macaques. In addition, infections or co-infection with B. pahangi (cats, dogs) or D. immitis (dogs) were detected. A novel Dirofilaria species was morphologically identified in 20.3% of macaques. Conclusions/significance Microscopy was less accurate for detection and species identification of Mf than qPCR. The presence of B. malayi Mf in animals represents a challenge for the elimination of LF in some areas in Indonesia. More research is needed to better understand B. malayi transmission between animals and humans in endemic areas like Belitung where routine MDA may not be sufficient to eliminate LF. © 2025 Diekmann et al.