Isolation of populations eventually leads to divergence by genetic drift, but if connectivity varies over time, its impact on diversification may be difficult to discern. Even when the habitat patches of multiple species overlap, differences in their demographic parameters, molecular evolution and stochastic events contribute to differences in the magnitude and distribution of their genetic variation. The Indonesian island of Sulawesi, for example, harbours a suite of endemic species whose intraspecific differentiation or interspecific divergence may have been catalysed by habitat fragmentation. To further test this hypothesis, we have performed phylogenetic and coalescent-based analyses on molecular variation in mitochondrial and nuclear DNA of the Celebes toad (Bufo celebensis). Results support a role for habitat fragmentation that led to a population structure in these toads that closely matches distributions of Sulawesi macaque monkeys. Habitat fragmentation, therefore, may also have affected other groups on this island.