Diversity of fungi from deep biosphere is recently gaining an increasing attention. We investigated fungal diversity in two sediment cores approx. 40 cmbsf (cm below seafloor) at a depth of approx. 5000 m in the Central Indian Basin (CIB), by culture-dependent as well as culture-independent approaches. This resulted in recovering a total of 19 culturable fungi and 46 operational taxonomic units (OTUs) respectively. Two of the cultured fungi showed similarity to Hortaea werneckii and Aspergillus versicolor, and 11 OTUs from environmental libraries showed high divergence (86-97 percent) from the existing sequences in the GenBank (NCBI database). Some of the fungi, such as Cerrena, Hortaea and Aspergillus sp., were recovered by culture-dependent as well as culture-independent approaches. Together, culture-dependent and culture-independent approaches detected a total of 12 distinct fungal genera and 42 OTUs respectively from two sediment cores indicating presence of a high fungal diversity in deep-sea sediments.