|The earliest Cape Muslims were brought to the Cape from Africa and Asia from 1652 to 1834. They were part of an involuntary migration of slaves, political prisoners and convicts, and they contributed in the ethnic diversity of the present Cape Muslim population. In addition to migrations, this population has grown by combined and continuous multiplex processes of intermarriage, natural increase, conversion and blending with other communities. Previous studies on the Cape Muslim population and local Cape Muslim communities have taken advantage of the huge amount of archival material covering the past three hundred years of Cape Muslim history in South Africa. The aim of this study, however was to investigate the genetic diversity and origins of one of these local Muslim communities, by taking advantage of the availability of modern molecular genetics tools. A pilot study conducted with Muslim volunteers residing all over the Cape Metropolitan area was used as a point of reference for the Kensington Muslim community study. Samples were investigated for DNA polymorphisms from both maternal (mitochondrial DNA) and paternal (Y-chromosome) in eages. Variations in these two types of DNA are grouped into continent-specific haplogroups or lineages. Six mtDNA and eight Y- chromosome SNP markers were screened using polymerase chain reaction- restriction fragment length olymorphisms (PCR-RFLP). Maternal lineages of Cape General Muslims were 34% African, 33% Asian and 33% European. The highest frequency for African lineages was observed in Cape Coloured Muslims (47%) and Cape Malay Muslims (45%). Cape Indian Muslims however displayed a higher frequency for Asian lineages (45%), while Cape Other Muslims for European lineages (50%). Paternal lineages indicated that 5% were of African descent, 75% Asian, 13% European and 7% of lineages remained undefined. Asian lineages were the most dominant paternal lineage with the highest frequency observed in Cape Indian Muslims (97%). In the second part of the study, contributions of major maternal African, Asian and European haplogroups to the Kensinglon Muslim community gene pool was investigated. This was achieved by examining mtDNA variations found within this community using twelve mtDNA coding region SNPs genotyped by the SNaPshot Mini sequencing assay. Maternal lineages of Kensington General Muslims indicated that 55% were of African descent, 34% Asiart, lYo European and 100% were of Eurasian descent. African lineages were the most frequent lineages of Kensington Coloured Muslims (56%), Kensington Malay Muslims (67%) and Kensington Other Muslims (100%). Kensington Indian Muslims maternal lineages were mainly of Eurasian origin (43%). The last part of the study investigated the contribution of the major male continent-specific lineages in the Y-chromosome diversity of the Kensington Muslim community by typing thirteen Y-chromosome SNP markers. Patemal lineages of Kensington General Muslims indicated that 4o/o were of African origin, 51% Asian and 45o% European. The highest frequency for Asian lineages was observed in Kensington Malay Muslims (56%), Kensington Indian Muslims (71%) and Kensington Other Muslims 11% (100%). However, Kensington Coloured Muslims paternal lineages were mainly of European origin (49%). The data obtained for Cape Coloured Muslims and Cape Malay Muslims and their Kensington Muslim counterpart's maternal and paternal gene pool were in agreement with historical findings concerning the origins of earlier Cape Muslims. Cape Indian Muslims and Kensington Indian Muslims maternal and paternal gene pool however demonstrated a strong accordance to mtDNA and Y-chromosome lineages observed in indigenous Indian populations.