Species identification in the genus Reticulitermes is often difficult because of ambiguous morphological characters. Challenges in Reticulitermes spp. recognition have also been encountered in East Asia, includingTaiwan. Because of unknown Reticulitermes taxa in Taiwan and the possible origin of alien Reticulitermes kanmonensisTakematsu in Japan and Korea, reexamining Reticulitermes fauna in Taiwan is imperative. To clarify the Reticulitermes fauna in Taiwan, this study applied two mitochondrial genes (cytochrome oxidase subunit II [COII] and 16S rDNA) and morphological characters for species delimitation. Reticulitermes specimens collected from 63 localities across the main and adjacent islands ofTaiwan were analyzed. Phylogenetic analyses, morphological comparisons, and ecological traits suggested the existence of three species inTaiwan: Reticulitermes flaviceps (Oshima), R. kanmonensis, and Reticulitermes leptomandibularis Hsia and Fan. Altitudinal distributions among the three Reticulitermes termites tended to differ: R. flaviceps adapted to low hills, but R. kanmonensis and R. leptomandibularis occurred in medium mountainous areas. The combined data, including haplotype diversities and distribution range, suggest that 1) R. flaviceps is an endemic species and only found in Taiwan; 2) R. kanmonensis and R. leptomandibularis are both native species in Taiwan and China; 3) Japanese R. kanmonensis populations originated from southern China and/or Taiwan and that Korean populations were possibly introduced from Japan.