There are growing examples of drug resistance in the fungal pathogens to evade antifungal drugs by developing mutation in the key targeted enzymes and high expression of drug transporter genes including ABC transporters and MFS transporters. This led to urgent need to identify novel (unique or essential to fungus) targets that can be used in development of potential antifungal drugs. We have used comparative genomics approach to find out novel targets in opportunistic fungus, Candida albicans responsible for severe infection in immunocompromised human. To identify novel targets we have analyzed available total 14,633 protein sequences (proteome) of C. albicans [SC5314] retrieved through RefSeq, an experimentally curated reference sequence database at NCBI, USA. To explore the unique proteins, proteome of C. albicans was first compared against human proteome and then with Saccharomyces cerevisiae (Yeast) through BLAST program (NCBI). Results showed that out of available 14,633 protein sequences of C. albicans, 4,568 were identified unique when compared against human, while 2,955 were identified unique when compared against S. cerevisiae.