Analyzing the genetic diversity of a population can be useful in identifying some of the silent effects of habitat fragmentation. We examined and compared 4 mitochondrial loci of the near threatened Short-tailed Babbler (Pellorneum malaccense), a rainforest understory bird, between a highly fragmented population in Singapore and populations from elsewhere in the Sundaic region. We found that the fragmented Singaporean population is genetically impoverished, with <20% of the intrapopulation genetic diversity present in a comparable sample from Borneo within intact forest. Differences in haplotype diversity among Singaporean sites of occurrence suggest that there may be extremely poor genetic diversity and connectivity among Singaporean subpopulations. These findings highlight the importance of connectivity in maintaining population genetic diversity in urban tropical forest patches. Our results also corroborate previous findings that there are 3 deeply diverged lineages of Short-tailed Babbler across the Sundaic region.