Genome reassortment and recombination mutations have been speculated to occur in infectious bursal disease virus (IBDV) and contribute to the emergence of new strains. However, evidence was lacking until recently when natural reassortant viruses were detected in China and Zambia. In this study, genome reassortment in African very virulent IBDVs was investigated by partial genomic sequencing, comparison of deduced amino acids and phylogenetic analyses. The findings revealed that the VP2 hypervariable region (VP2-HVR) and part of VP1 corresponding to 332 amino acids of the N-terminus were the best representative of the entire genome segments A and B of IBDV, respectively. The part of VP1, which spans the one-third of segment B to the 5’-end revealed 5 amino acid positions (61, 145, 147, 219 and 242) to be critical for the evolution of genome segment B. Taken together, these findings indicate that partial molecular characterization of segments A and B could be used for examination of genome reassortment and recombination mutations in IBDV.