The novel species Metschnikowia shivogae is described to accommodate three isolates recovered from insects of morning glory flowers at two localities in East Africa. The isolates differ slightly in rDNA ITS and D1/D2 large-subunit sequences and one isolate featured a two-base heterogeneity that might be the result of recombination between two variant rDNAs. M. shivogae is a sister species to Metschnikowia aberdeeniae and shares the same habitat. The reproductive boundaries of M. aberdeeniae, which were not clear in the past, have now been elucidated further. The type strain of Metschnikowia shivogae sp. nov. is strain SUB 04-310.1T (h +; =CBS 10292T =NRRL Y-27924T) and the allotype is strain UWOPS 07-203.2 (h −; =CBS 10770 =NRRL Y-48447).