Due to the nature of the marine environment genetic studies allow insight into behaviour and natural history that is difficult or impossible to identify by direct field observation. Current as well as historical population demography and gene flow can be detected by using molecular techniques. Genetic studies on only a few commercially important marine species along the South African coast have been conducted, although many marine fish species utilize estuaries as nursery areas and little attention has been afforded to studying larval distribution and recruitment of these species from a molecular point of view. Many of these estuarine associated species, especially in the South African milieu, are important for recreational and subsistence use. Associated with southern African estuaries are 13 species of the family Sparidae of which Cape stumpnose Rhabdosargus holubi is the most abundant. Juveniles are mostly confined to estuaries while the adults are strictly marine. Rhabdosargus holubi are serial spawners but temporally separated spawning peaks have been recorded along the South African coastline. Within the first part of this dissertation, the general characteristics of marine fish populations and the marine environment along the South African coast are being discussed. The main aim of this study was to determine the population genetic structure from estimates of nuclear and mitochondrial genetic variation across the distributional range of Rhabdosargus holubi. Samples were collected from 13 geographic localities along the South African coastline from St Lucia in the northeast to Klein River in the southwest. Juveniles were sampled in estuaries and adults were collected in the marine intertidal zone. Mitochondrial DNA control region fragments of 368 bp in length were obtained from a total of 214 individuals from all sampling localities. A total of 36 alleles were identified from 34 polymorphic sites. Following an allele homogeneity test, samples from different localities were lumped to represent six distinct geographical regions. Mitochondrial DNA control region analyses of juveniles showed high haplotype diversity and low nucleotide diversity with no divergent maternal lineages. No pattern between haplotype genealogy and geographic locality was evident. Population genetic analyses using heterologous microsatellite amplification have been successfully completed for a number of studies, including numerous studies of variation within marine fish species. Microsatellite studies have proven to be more sensitive in detecting subtle population structure than mtDNA and/or protein polymorphisms in high gene flow species. A total of 113 microsatellite loci previously isolated from phylogenetically closely related marine fish species were tested for amplification. The success rate of heterologous microsatellite amplification was extremely low (0.02%), with only two polymorphic loci amplifying consistently for analysing 133 individuals sampled from six localities along the distributional range of R. holubi. Results from these two loci were insufficient to draw conclusions about the population genetic structure of R. holubi along the South African coast. Possible reasons for the low rate of amplification success and future research recommendations are discussed. The findings from this study suggest that R. holubi is not geographically restricted, has high gene flow among localities and likely exist as a single stock. / Dissertation (MSc (Genetics))--University of Pretoria, 2006. / Genetics / unrestricted