Holy basil or its scientific name Ocimum sanctum L. seedlings were grown both in Japanese Experiment module in the International Space Station (ISS) and ground control (earth) for 30 days duration. Plant samples were placed in closed environment incubator under control light, temperature, humidity and CO2 conditions, before bring back to earth. Pool of first leaf and stem were RNA extracted and sequenced. The sequences were allligned to reference genome O. basilicum. We identified differential express genes of holy basil ISS vs ground control with total of 1518 (up regulated)/ 1046 (down regulated) for leaf and 599 (up regulated)/224 (down regulated) for stem. The top 10 upregulated and downregulated genes in leaf/stem ISS vs ground control with more than two fold in gene expression was selected and their possibility of gene function in microgravity environment. The differential express gene were analysed for Gene ontology (GO) enrichment. The top 3 prominent GO enrichments for holy basil leaves were cytosol, chloroplast and cytoplasm, while GO enrichment for stems were cytosol, cytoplasm and golgi apparatus. The top 3 differential genes for Kyoto Encyclopedia of Genes and Genomes (KEGG) for leaves were metabolic pathway, biosynthesis of secondary metabolites and microbial metabolism in diverse environment, while KEGG enrichment for stems were endocytosis, photosynthesis-antena protein and photosynthesis.