Terpenoids are synthesized in plants through the mevalonate (MVA) and the methylerythritol phosphate (MEP) pathways, among isopentenyl diphosphate (IPP) as the central intermediate metabolite. 3-Hydroxy-3-methylglutaryl- Coenzyme A synthase (HMGS) is a subsequent enzyme in MVA pathway of isoprenoid biosynthesis and catalyses the condensation of acetyl-CoA by acetoacetyl-CoA to yield HMG-CoA. Different genes of HMGS are present in different species of plants and animals for the synthesis of secondary metabolites. The present study was planned to compare and analyse bioinformatically the HMG-CoA gene sequence of Brassica rapa with other sequences of different species. The gene sequence have 925 bp coding DNA sequence and was submitted in National Centre for Biotechnology Information (NCBI) with accession Number. MF577077. The alignment of nucleotide and protein sequences was carried out through Geneious. Bioinformatics comparison including structural and functional analysis of HMG-CoA synthase like gene sequence isolated from Brassica rapa was carried out by using different bioinformatics tools and softwares. These comparisons gave a better information about properties, genetic and functional diversity of this gene along with amino acid substitutions.