Houtman’s Abrolhos, off the coast of Western Australia. The remains are now stored in the Western Australia Maritime Museum (WAMM) in Fremantle. In this research an attempt is made to type ancient DNA (aDNA) from the remains of the Batavia Mutiny, which are almost 400 years old. Previous anthropological studies have been performed on these remains in order to assign sex, age and stature. The aim of the present project is to study the familial relationships of the remains and to determine their sex based on molecular genetic analysis. In order to protect the invaluable museum specimens and minimise the risk of contamination from exogenous contemporary DNA, a tooth sample from each available individual (designated A15507, A16316, A15831, M3901, SK5, SK6, SK7, SK8 and SK9) was subjected to DNA extraction. Comparison and optimisation of DNA extraction methods from more recent teeth samples was performed in order to determine the most suitable method for the DNA extraction of the ancient teeth samples. Three types of genetic markers were analysed in an attempt to study the familial relationships and determine the sex of each individual. Multiplex primers (Hummel, 2003) which simultaneously amplify the HV1 and HV2 regions of mitochondrial DNA (mtDNA) were used in this research to analyse familial relationships. These primers were selected because of their ability to amplify small fragments (131bp, 168bp and 217bp) of DNA template, which suit the nature of aDNA samples. Primers published by Sullivan et al.(1993), which amplify a 106bp region on chromosome X and 112bp on chromosome Y of the amelogenin gene, were used to determine sex. In addition, short tandem repeat (STR) marker were also analysed to determine familial and sex using the AmpFlSTR®Profiler PlusTMPCR kit from Applied Biosystems. The PCR conditions of all primers were optimised before usage on the Batavia remains. As aDNA analysis is prone to contamination, stringent precautions were undertaken throughout this research. Despite this, contamination is suspected in some of the mtDNA sequences obtained (particularly from SK5, SK7, A15507 and A15831), which most probably came from the positive control used in the optimisation analysis. For these samples the sequences for the HV2 region were poor and polymorphisms relative to a reference were similar to each other and to the positive control profile. However, some conclusions have been made on other individuals (SK8, SK9, M3901, A16316) based on the HV1 and HV2 sequences obtained. Based on two or more different polymorphisms observed in the individuals it was concluded that it is likely there is no maternal relationship between individuals A16316 and SK8, SK9 and M3901 and between individuals SK8, M3901 and SK9. However these results require repetition for confirmation. The attempt to type the amelogenin gene on chromosomes X and Y was unsuccessful most likely due to the poor preservation of the remains. It is apparent from this research that although it was possible to extract aDNA (especially multicopy mtDNA) from teeth material that were almost 400 years old, the main hurdle in this aDNA analysis was contamination and DNA degradation.