In 2017 a survey was conducted of the Drosophilidae on the remote Cook Islands: Rarotonga, Aitutaki and Mangaia in the Tropical South Pacific. A diverse range of collecting methods was implemented, at different elevations and in domestic, rural, and montane-forest habitats. Only two widespread species Drosophila ananassae and D. simulans have previously been reported from Cook Islands. Among the 8036 specimens collected, 12 species were found, one of which—Drosophila rarotongae sp. nov.—is described here as new; it is endemic to Rarotonga and found only in montane forest. Drosophila suzukii was absent. An unusual species close to Drosophila funebris was collected (one female); various measures revealed its morphological difference from Afrotropical and Palaearctic D. funebris specimens. Possible synonymies between Scaptodrosophila bryani and S. anuda, and between S. concolor and S. marjoryae were discovered and are discussed. Drosophila pallidifrons was found among D. sulfurigaster in very low frequency (1%).