Thesis (MSc)--Stellenbosch University, 2010. / ENGLISH ABSTRACT: Opisthopatus cinctipes is a velvet worm endemic to South Africa and is widely distributed in isolated Afromontane and coastal forest patches throughout the Eastern Cape, KwaZulu-Natal and Mpumalanga. The species, like most velvet worms is characterized by low vagility, microhabitat specialization and is hypothesized to harbor significant cryptic diversity. We used partial sequence data derived from three partial mitochondrial (mtDNA) gene loci (COI, 12S rRNA and 16S rRNA) and a partial nuclear gene fragment (18S rRNA), as well as gross morphological character analysis and scanning electron microscopy (SEM) to determine evolutionary relationships amongst a total of 120 specimens of O. cinctipes from 33 localities. Phylogenetic relationships were investigated using Bayesian inferences, Maximum Parsimony and Maximum Likelihood analysis. Phylogenetic analysis of mtDNA and nDNA data revealed the presence of multiple cryptic lineages nested within Opisthopatus cinctipes with at least nine distinct well supported clades (> 70% / > 0.95 pP), suggesting that the taxon comprises a “species complex”. Afrotemperate forest specimens were genealogically highly distinct from each other whilst Indian Ocean Coastal Belt forest (at least in KwaZulu-Natal) specimens were more closely related and formed a well supported clade. An analyses of molecular variance indicated that (ΦST) 89.31% of the genetic variation occurred amongst localities. Highly significant FST values were generally observed across sampled localities (FST = 0.89, p < 0.001). Tajima’s D value was 0.83 over all sampled localities, implying a decrease in population size and/or balancing selection. Uncorrected pairwise sequence divergence values between O. cinctipes localities for the COI locus were high and ranged from 3.20% to 19.50%. No haplotypes were shared between localities. There is considerable evidence showing that past geological events may have shaped the deep genetic divergences observed between sampling localities suggesting the absence of gene flow. Genetic divergences within the South African O. cinctipes species complex are shown to have occurred from the onset of the Cenozoic era. The genetic variation observed within clades was not accompanied by morphological differences suggesting that the use of morphological characters has grossly underestimated species diversity within South African Opisthopatus. A robust taxonomic documentation of the species diversity within the O. cinctipes species complex is critical for the implementation of conservation management plans for this species complex. We recommend that highly sedentary taxa with limited dispersal abilities and specific habitat requirements which may be found in sympatry with velvet worms be prioritized for taxonomic revision as they may also harbor cryptic lineages. / AFRIKAANSE OPSOMMING: Geen Afrikaanse opsomming beskikbaar.