Brugia timori is widely distributed on Alor Island, Indonesia, where it causes a high degree of morbidity. The HhaI tandem repeat of B. timori was found to be identical to that of B. malayi, for which sensitive PCR-based assays have already been developed. Using one of these assays, a single microfilaria (mf) of B. timori, present in a spot of dry blood on filter paper, could be detected. The assay was equally sensitive in the detection of B. timori and B. malayi. When the collected mosquitoes were pooled according to species and tested with the assay, 39 (64%) of the 61 Anopheles barbirostris pools (containing a total of 642 mosquitoes) were positive. As none of the 33 Culex pools tested (which contained 624 mosquitoes) gave a positive result, and An. barbirostris is the only Anopheles species commonly caught on human bait in Alor, An. barbirostris is assumed to be the main and perhaps only local vector. Brugia timori could be differentiated from B. malayi by restriction-endonuclease digestion of the PCR-amplified mitochondrial cytochrome oxidase subunit 2. A few distinct nucleotide exchanges were also found in the second internal transcribed ribosomal spacer of the filariae, and in the 16S rDNA and FTSZ gene of their Wolbachia endobacteria. The results show that B. timori can be effectively detected using the PCR-based assay developed for B. malayi and can then be differentiated from B. malayi by other molecular markers. PCR-based techniques targeting the HhaI repeat can therefore be employed for monitoring B. timori in the framework of the Global Programme to Eliminate Lymphatic Filariasis.