Use of insects in forensic science needs a correct identification of insects to correlate their decomposition rate with post mortem interval. This study emphasizes on puparia based identification of Chrysomya megacephala with C. rufifacies of a road cadaver of a dog found at Osmanabad district, Maharashtra, India. Scanning electron micrographs of both species were studied to differentiate them. Distinguishing characteristics of both species observed during present study are pattern of folding in frontal field, number of anterior spiracles, posterior spiracles, number of tubercles, and structure of button, spiracular hair and middle sacrum. This study provides a comprehensive key to identify fly species using scanning electron micrographs of puparium.