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Chironomid head capsules were identified from sediment cores taken from Lake Gokyo (4750 m) and Lake Gosaikunda (4350 m) in the east-central Himalaya, to determine taxonomic composition of chironomid assemblages over time. The sedimentation rate of Lake Gosaikunda was estimated at 0.05 cm/yr and that of Gokyo was estimated at 0.07 cm/yr by 210 Pb and 137 Cs dating. Micropsectra sp. was dominant in the sediments of both lakes. Lake Gokyo sediments also contained Pseudodiamesa sp., Eukiefferiella/Tvetenia sp., Orthocladius/Cricotopus sp. and Rheocricotopus sp. The concentration of headcapsules was nearly an order of magnitude greater in the Lake Gosaikunda core, which contained mostly Micropsectra sp. and Pseudodiamesa sp. These taxa are typical of cold oligotrophic lakes. Differences in lake depth, dissolved minerals, plus epi-and hypolimnetic temperature and dissolved oxygen suggest that stratification and temperature-induced increases in primary production may affect chironomid assemblages in these pristine lakes. Palaeolimnological studies of Himalayan lakes should include replicate cores within lake, to increase headcapsule sample sizes given potentially high rates of sedimentation from glacial runoff.