An anatomical study of Microbrachis reveals inaccuracies in previous studies, especially in the palate and cranial proportions. The vomer and the pterygoid reach the midline anteriorly, and the postorbital does not appear to reach the tabular. The skull is higher in our cranial reconstruction than previously thought. A phylogenetic analysis of early stegocephalians places Microbrachis at a fairly basal position in the clade that includes “microsaurs,” lysorophians, and lissamphibians. This analysis corroborates previous suggestions that lissamphibians are part of a clade that includes the taxa classically referred to as “lepospondyls,” and that seymouriamorphs and temnospondyls are not part of Tetrapoda. Statistical tests on another recent amphibian phylogeny reveal that its different placement of the origin of lissamphibians is not statistically more parsimonious than the placement that we suggest. Our analysis also suggests that the first evolutionary radiation of amphibians took place in an aquatic environment because most of the first groups of amphibians to have differentiated, namely adelogyrinids, nectrideans, and Microbrachis, appear to have been aquatic or amphibious taxa. However, the lifestyle of many early amphibians is difficult to assess.