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Indonesias oceans are rich in microalgae as unicellular photosynthetic organisms. So far, most of Indonesias diverse microalgae have yet been explored. An Isolate NBO of microalgae has been collected from the beach of Pulau Bokor in the Jakarta bay. This study aimed to identify the isolate NBO and to characterize its biochemical properties. The identification was carried out based on the physical morphology of cell and the genetic type of 18S rDNA V4 and LSU D2/D3 regions, meanwhile the biochemical properties were characterized based on the content of carbohydrate, lipid and fatty acid of cells. The results showed that NBO cells had a color of yellow-brown, a shape of oval with ranging from 11.00 – 15.00 μm in length and 4.67 - 5.00 μm in width, and a silica frustule that bilaterally symmetrical oval. These morphological characteristics identified the isolate NBO under genus Navicula. Genomic regions of 430 bp of 18S rDNA V4 and 603 bp of LSU D2/D3 were obtained and both showed highest nucleotide sequence similarity with Navicula salinicola (GenBank no. GQ219689.1; HQ396812.1), i.e. 99% and 98% respectively. The microalgae isolate was identified as Navicula salinicola NBO. Analysis of cell biochemical compounds resulted a total content of carbohydrates and lipids respectively about 13.13% (w/w) and 3.74% (w/w) of dried biomass. The lipids composed of 40.94% SFA (saturated fatty acid), 40.05% MUFA (mono-unsaturated fatty acid), and 19.01% PUFA (Polyunsaturated fatty acid) with Omega-3 content (18.45%), Omega-6 (0.59%), and Omega-9 (2.82%).