278Hydrogenase is an enzyme that catalyzes the reversible oxidation of molecular hydrogen (H2). Here, the hydrogenase enzyme structures of Chlamydomonas reinhardtii, Clostridium pasteurianum, and Desulfovibrio vulgaris were taken as reference. Homology structures of the hydrogenase enzymes taken from Clostridium acetobutylicum, Chlorella variabilis, and Scenedesmus obliquus were developed. BLAST search was performed and the templates with a minimum of 35% sequence similarity were considered for homology modelling. Structure analysis was performed after minimizing the energies of the nine (3*3) structures. For analyzing the gas diffusion path and hydrogen bonds, C. pasteurianum (CpI) was taken as the reference. It has been seen that the path was formed around the H-cluster which was where the hydrogen molecule was produced. It was blocked by the oxygen molecule in its path reducing the efficiency of the enzyme. With this information we selected C. variabilis as the next model organism along with C. reinhardtii for our further research to study the exact mechanism of gas diffusion in the enzyme.