The data is for insect samples from Malaise traps in Mengsong, Xishuangbanna, Yunnan Province, China. Samples were prepared by using one leg from all specimens equal to or larger than a large fly (~5 mm length) and whole bodies of everything smaller. Following the protocol of Ji et al. (2013), samples were homogenized, and DNA was extracted, quality-checked, PCR-amplified with indexed, degenerate primers for the standard mtCOI barcode region, and gel-purified. The PCR products were A-amplicon-sequenced on a Roche GS FLX at the Kunming Institute of Zoology. The 28 Mengsong samples were sequenced on one whole run (four 1/4 regions, November-December 2010: wet season) and two 1/4 regions (May-June 2011: dry season), producing 519 865 and 253 025 raw reads, respectively
