In this study we report the first animal invasion, to our knowledge, into Lake Malawi. The colonizer is a non‐native morph of the gastropod Melanoides tuberculata that differs substantially in external shell characters from co‐occurring indigenous forms. However, because the species possesses extensive within‐Africa geographical variation in shell morphology, it was unclear whether the invasion was range expansion of a native African morph, or a colonization from elsewhere. Mitochondrial DNA sequences indicate a southeast Asian origin for the invader, suggesting that shell variation found among indigenous allopatric populations camouflaged an intercontinental invasion.