Abstract
Marbled lungfish Protopterus aethiopicus in Lake Victoria and two nearby smaller lakes were found to have high levels of DNA sequence variation in their mitochondrial control regions (35 haplotypes in 61 fish) but no population genetic structure (Φ ST = 0·00). In contrast, marbled lungfish in Lake Baringo, Kenya, appeared to be fixed for a single control region haplotype, which occurred at low frequency in the other lakes. Using FLUCTUATE software, the female effective population size in Lake Victoria during the late Pleistocene was estimated to be c. 500 000, similar to the value estimated for the present‐day population. These observations suggest that, during the late Pleistocene dry period, a large marbled lungfish population survived either in wet refugial areas within the lake basin or in surrounding areas. Marbled lungfish were reported to have been introduced into Lake Baringo 30 years ago with a founding population of only three individuals. The lack of control region variation in the Lake Baringo population is consistent with that situation.