Abstract: Circadian clocks are dependent on multiple transcribed genes which control gene expression levels. These genes belongs to cryptochrome family and mainly includes Cry 1 and Cry 2 genes and also specialized falvoproteins. Cry1 gene was found to play an important role in maintaining energy balance under various nutritional circumstances. The circadian system is responsible for regulating a wide variety of physiological and behavioral rhythms. The analysis of these genes predicted regions of high similarity among both selected homo sapiens and mouse Cry 1 gene. The results were obtained by using BLAST tool. Phylogenetic analysis of Cry 1 gene was performed by CLUSTA W alignment software. Protein domains were analyzed by using Interpro domain repository. Therefore, the analysis through bioinformatics tools can be useful to infer 3D structure and function of proteins.