Biodiesel has turned into the need of the hour with the massively expanding transportation sector. With the shrinking scope of fossil fuel reliance newer options such as green plants were targeted as the alternative source. The first and second generation biofuel resources comprised the edible and non-edible plants. Since these plants were competing with the food and land availability the third generation biofuel source was selected meticulously to overcome these disadvantages. Thus algae were the ultimate choice as its growth requirements were limited to marine or freshwater, least fertile terrain and sunlight. Several algal species, including both macroalgae and microalgae are studied extensively for their hydrocarbon producing capacity. Sargassum, Chlorella vulgaris, Botryococcus braunii, Chlamydomonas and Desmococcus olivaceous are some of the algal species which are targeted for various reasons. Botryococcus braunii is a green, microalgae known for its high hydrocarbon content. In this study, we have attempted to analyze the transcriptome data of two races of B braunii. The transcriptome data was subject to pre-processing as it contains some low quality reads. After the quality check the obtained high quality reads were assembled using Trinity transcriptome assembler. The short reads were assembled into contigs. These contigs were further annotated using BlastX. The reads with the homologous hits were analyzed for the presence of enzymes involved in the hydrocarbon biosynthesis. Hence, in this study, we were able to map the transcripts corresponding to the enzymes involved in various pathways.