The muscle pattern of malacostracan and entomostracan crustacean nauplius larvae was compared using fluorescent phallotoxins. In the dendrobranchiate malacostracan Sicyonia ingentis, F-actin staining was first detected in limb setae at 12 h, likely within sensory nerves. Staining of F-actin was detected in the trunk at 15 h and grew into the naupliar limbs. Sarcomeres were detected at 19 h, identifying the structures as extrinsic limb muscles. The extrinsic limb muscles enlarged but retained their general pattern during the later nauplius stages. Longitudinal trunk muscles and circumferential visceral muscle (VM) developed in the post-naupliar region during nauplius instars 4 and 5, at the time when the gut also formed. In the anostracan branchiopod Artemia salina, the newly hatched nauplius contained an extensive system of extrinsic and intrinsic limb muscles. The gut was almost complete at hatching, along with its associated circumferential VM. Muscles similar in position and structure could be identified in nauplii from the two taxa, but different anatomical origins of extrinsic muscles were evident. Whether the naupliar limb muscles are homologous in malacostracans and branchiopods remains an open question. The strong musculature of the dendrobranchiate naupliar limbs correlates with the use of all three pairs of limbs for swimming.