The Popeye domain containing (Popdc) genes encode a family of transmembrane proteins with an evolutionary conserved Popeye domain. These genes are abundantly expressed in striated muscle tissue, however their function is not well understood. In this study we have investigated the role of the Popdc2 gene in zebrafish. Popdc2 transcripts were detected in the embryonic myocardium and transiently in craniofacial and trunk muscles. Morpholino oligonucleotide mediated knockdown of Popdc2 resulted in aberrant development of skeletal muscle and heart. In the trunk, fast and slow muscle types were normally distributed but the myofibers displayed misalignment. The morphants showed circular swimming behaviour upon stimulation suggesting that theaberrant muscle structure caused abnormal muscle function. Craniofacial muscles were more severely affected by the absence of Popdc2, since many facial muscles were absent. The hearts were also severely affected by the loss of Popdc2 showing massive oedema and abnormal heart looping in the morphants. After reducing the morpholino concentration cardiac oedema and abnormal looping were normalized, however the morphants now displayed a cardiac arrhythmia phenotype,which first became apparent at day 3 of development. Optical recordings of cardiac contractility revealed the presence of an arrhythmia phenotype, characterized by irregular ventricular contractions with a 2:1, or 3:1 atrial/ventricular conduction ratio, which caused a significant reduction in heart frequency. Recordings of calcium transients with high spatiotemporal resolution using a transgenic calcium indicator line (Tg(cmlc2:gCaMP)s878) and SPIM microscopy confirmed the presence of a severe arrhythmia phenotype, which probably was caused by premature atrial depolarization. In older animals complete dissociation of atrial and ventricular contraction and even a complete heart block was observed. Our results identify Popdc2 as a gene important for cardiac and skeletal muscle development.