The micro frog, Microbatrachella capensis (Boulenger, 1910), is a Critically Endangered anuran found in fragmented marshland habitats along the southern coast of the Western Cape Province of South Africa. The genetic diversity between and within the remaining populations (Kenilworth, Grootwitvlei, Kleinmond, Lamloch, Hagelkraal, and Buffeljacht/Ratelrivier) of Microbatrachella capensis in the Western Cape Province of South Africa was assessed, sampling 12 specimens from each population. Genetic diversity was determined from an analysis of mitochondrial DNA sequences obtained from the ND2 gene region/locus. A phylogeographic analysis of the populations of micro frogs sampled was used to determine the current genetic structure and the history of the species. The analysis divided the six populations of the species into two lineages. The variation within the populations ranged from two to six haplotypes per population. Nested clade analysis inferred allopatric fragmentation for three out of the five significant clades. The division of the lineages into two geographical units, the absence of gene flow and the allopatric fragmentation indicates long-term isolation, around 1.09-1.52 my ago. The isolation and fragmentation of the populations is postulated to be due to historical sea level fluctuations that occurred in Southern Africa during the Quaternary Period. Allopatric fragmentation and lack of gene flow among populations within the two major lineages are due to recent habitat destruction through development. The recognition that the species contains two evolutionarily significant units, corresponding to Agulhas and western lineages, will aid future conservation efforts to save this species. / Dissertation (MInstAgrar)--University of Pretoria, 2005. / Zoology and Entomology / unrestricted