Candida africana is emerging as an organism of interest. It is evolutionarily divergent from Candida albicans but has reduced virulence with a restricted ecological niche. This study aimed at comparing in silico the genome level to detect variations in the two species. Raw Illumina Hiseq data were downloaded from the European Nucleotide Archive (https://www.ebi.ac.uk/ena) with the accession number SRR6669859 and assembled using shovill (v. 1.0.9) the resulting genome was mapped against the haploid reference Candida albicans SC5314_A22 strain using the D-GENIES webtool and contigs were reordered based on the reference, then gap-filled using GapFiller (v1-10), and annotated using MAKER-P. Synima and progressive Mauve were used to compare the annotated genomes of Candida africana and Candida albicans for synteny. OrthoVenn2 webserver was used for the identification and comparison of orthologous clusters. Microsynteny variations within the genomes were determined using the GEvo. The study revealed the presence of insertions, deletions, and hypervariable regions within the genome of Candidia africana, showing a high level of synteny with Candida albicans. The genome of Candida africana is 14.04Mbp with a BUSCO score of 99.66%. The two species form a total of 5146 orthologous protein clusters and shared a total of 5124 protein, C. africana has a unique cluster protein cluster while C. albicans have 18 unique Protein clusters. The genome of C. africana has lots of structural variations and the presence of gene losses and gains. These genetic variations possibly play a role in the reduced virulence potential observed in C. africana.