We present a comparison of the development of trunk limbs in Nebalia sp. (Leptostraca) and Limnadopsis parvispinus (Branchiopoda). The overall correspondence in specific developmental steps and morphology, e.g., size and orientation of limb anlagen, plus the resulting interpretation of adult limb part homologies lead to the suggestion that phyllopodous limbs in Leptostraca and Branchiopoda are homologous. In addition, our data allow the conclusion that the branchiopod limb forms a three-lobed rather than an undivided endopod. During early development of Nebalia sp. the pleopods form a transitory, putative, and vestigial epipod. The presence of this epipod on the pleopod lends support to the idea that the tagmatisation of the malacostracan trunk into thorax and pleon is the result of a secondary subdivision of an ancestral crustacean thoracic region.