Microalgae can serve as a better feedstock for biodiesel leading to an alternate renewable energy resource, while algal strains which serve as a feedstock for biodiesel and bioactive pigments are scarce. Herein, we report the draft genome sequence and gene predictions of one such novel microalgal isolate Coelastrella sp. M-60 for the first time. The genome assembly is of ~80.2Mb size having 8163 predicted genes which revealed the presence of putative genes concerned with efficient nutrient uptake, bioremediation, in addition to lipid and carotenoid accumulation. Diverse unicellular algae of Chlorophyta, Rhodophyta and Phaeophyta have been reported for lipid and pigment biosynthesis and the predicted proteins of Coelastrella sp. M-60 showed substantial similarity with the aforementioned phyla. Differential expression analysis by real-time PCR regarding genes involved in the lipid and pigment biosynthetic pathways of Coelastrella sp. M-60 under osmotic stress conditions showed considerable upregulation in their transcript levels. The genome sequence availability of this potent microalga would enhance its utility through genetic manipulation strategies and help in deducing the mechanism of high value products accumulation in future. Display omitted •Coelastrella sp. M-60, a new microalgal isolate accumulates hyper lipids and carotenoids in stress at hot outdoor conditions.•Genome sequence assembly and transcript profiling of lipid & carotenoid biosynthesis of Coelastrella sp. M-60 were reported.•This investigation uncovers its genome for the potential genes for various application for the first time.•TAG and carotenoid pigment biosynthetic pathways were proposed for Coelastrella sp. M-60 through genome annotation.