Proper mitochondrial morphogenesis is crucial for successful development of motile sperm. It was known that recessive Drosophila melanogaster mutation emm caused anomalies in the formation of a mitochondrial derivative--nebenkern and led to male sterility. Here we identified primary mutation effect and showed that emm is required for the formation and maintenance of inner mitochondrial structure starting from early spermatocytes. Abnormal mitochondria structure affects subsequent cellular processes in spermatogenesis such as meiotic cytokinesis and spermatid elongation.