Apomixis, or asexual seed development, if introduced into crop species, has the potential to greatly improve global food production. Towards this goal, this study focused on uncovering the genetic mechanisms that control the parthenogenesis step within apomixis whereby fertilisation is avoided. In the model apomict, Hieracium praealtum (Asteraceae), parthenogenesis is controlled by the LOSS OF PARTHENOGENESIS (LOP) locus. Previous research showed that in addition to genomic copies of candidate genes at LOP, the genome has at least three other copies referred to as alternative alleles. The main goal of this study was to investigate four candidate genes, Genes B, X, H and Y, at LOP by generating segregation data of the alternative alleles. BAC clones containing alternative allele sequences were identified and Roche 454 pyrosequenced. These sequences were used to design alternative allele specific primers for genotyping two Hieracium praealtum polyhaploid populations (~ 300 plants). Four major conclusions were drawn from this study. First, the alternative alleles were in fact acting like alleles to the LOP alleles of Genes B, X and Y. Second, allelic sequence divergence (ASD) of the LOP alleles of Genes B and X relative to the alternative alleles, indicated a recent and separate evolutionary history. Third and, unexpectedly, recombination was detected at the LOP locus, in contrast to other apomixis loci reported in the literature. Furthermore, Gene B was found to be very closely associated with parthenogenesis in the polyhaploid population indicating that it may be essential to parthenogenesis and therefore requires further investigation. On the other hand, the absence of Genes X, Y and H, due to recombination, had no impact upon parthenogenesis. Fourth, the sequence data suggested that the LOP and alternative alleles originated from a shared common allele ancestor. It is hoped that these findings have made a significant contribution towards the future goal of introducing apomixis into crop species.