Filamentous fungus Aspergillus niger has gained significant industrial and ecological value due to its great potential in enzymatic activities. The present study reports the complete genome sequence of A. niger BSC-1 which was isolated from Indian Sundarban mangrove ecosystem. The study revealed that the genome of A. niger BSC-1 was 35.1 Mbp assembled in 40 scaffolds with 49.2% GC content. A total of 10,709 genes were reported out of which 10,535 genes were predicted for encoding the proteins. BUSCO assessment showed 98.6% of genome completeness indicating high quality genome sequencing. The genome sequencing of A. niger BSC-1 revealed the presence of rodA and exgA genes for initial adhesion to surface and Ags genes for matrix formation, during biofilm growth. OrthoVenn2 analysis revealed that A.niger BSC-1 shared 9552 gene clusters with the reference strain A. niger CBS554.65. Semi-quantitative RT-PCR analysis unveiled the role of Ags1 and P-type ATPase in fungal biofilm formation and chromium (Cr) resistance, respectively. During biofilm growth the expression of Ags1 significantly (P < 0.0001; two-way ANOVA followed by Sidak’s multiple comparisons test) increased with respect to planktonic culture revealing the possible involvement of Ags1 in biofilm matrix formation. Expression of P-type ATPase gene was significantly upregulated (P < 0.0001; one-way ANOVA followed by Dunnett’s multiple comparisons test) with the increasing chromium concentration in the fungal culture. Besides, several other genes encoding metalloprotease, copper and zinc binding proteins, and NADH-dependent oxidoreductase were also found in the genome of A. niger BSC-1. These proteins are also involved in heavy metal tolerance and nanofabrication indicating that this filamentous fungus A. niger BSC-1 could be potentially utilized for chromium detoxification through biofilm or nanobiremediation.