In the Drosophila embryo, nautilus is expressed in a subset of muscle precursors and differentiated fibers and is capable of inducing muscle-specific transcription, as well as myogenic transformation. In this study, we examine the consequences of nautilus loss-of-function on the development of the somatic musculature. Genetic and molecular characterization of two overlapping deficiencies, Df(3R)nau-9 and Df(3R)nau-11a4, revealed that both of these deficiencies remove the nautilus gene without affecting a common lethal complementation group. Individuals transheterozygous for these deficiencies survive to adulthood, indicating that nautilus is not an essential gene. These embryos are, however, missing a subset of muscle fibers, providing evidence that (1) some muscle loss can be tolerated throughout larval development and (2) nautilus does play a role in muscle development. Examination of muscle precursors in these embryos revealed that nautilus is not required for the formation of muscle precursors, but rather plays a role in their differentiation into mature muscle fibers. Thus, we suggest that nautilus functions in a subset of muscle precursors to implement their specific differentiation programs.