Myocyte enhancer factor 2 proteins are members of MADS family of transcription factors, which can control the expression of muscle-specific genes in vertebrates. However, not all Mef2 genes are essential for muscle development in invertebrates. Here we have isolated a full-length cDNA from amphioxus, designated AmphiMef2. The predicted amino acid sequence has highly conserved MADS and MEF2 domains, showing higher identity with the corresponding regions of its homologues in vertebrates than those in invertebrates. Results from whole-mount in situ hybridization show that the expression of AmphiMef2 initially appears in the presomitic mesoderm at early neurula stage, then the transcripts are detected in both the somites and the unsegmented presomitic mesoderm. At 36 h larval stage, the expression is only detected in the posterior somites. By 48 h larval stage, the expression is shifted to the preoral pit (a homologous organ to the vertebrate adenohypophysis) and persists until at least 72 h larval stage. The results suggest that AmphiMef2 may be not only involved in the myogenesis but also the development or function of the preoral pit in amphioxus.