<p>We investigated the development of the metanephridial system in larval and post-metamorphic stages of a model animal, the mussel <i>Mytilus</i> by a correlative LM, TEM and 3D approach. Part of the system is already functional in the veliger stage, before the foot is formed. Functionally, this is a pair of protonephridia, in addition to the anterior larval protonephridia, with which it significantly overlaps in its temporal occurrence. This is the first clear evidence for such transitory organs in molluscs. The organs consist of a kidney part and a small bulb with a regular ultrafilter. A ciliary flame emerges from the bulb extending into a duct that opens into the kidney part. The kidney part is already formed similarly to the adult kidney that it will become in further development. Later in development, these protonephridia are incorporated into the metanephridial system. The ultrafiltration bulb is integrated into the pericardium and heart, which arise from a different anlage in post-metamorphic development. Nephrogenesis in <i>Mytilus</i> is completely different from that of a previously investigated polyplacophoran, suggesting that ontogenetic processes in molluscan nephrogenesis should not be overestimated with respect to homology questions. Nevertheless, the nephrogenesis of <i>Mytilus</i> refutes arguments against a homology of the metanephridial system of molluscs with that of other invertebrate phyla, such as the annelids, due to the independent formation of the releasing parts. Other aspects are discussed, such as the temporal overlap of larval protonephridia and the metanephridial system, the function of transitory protonephridia, the distribution of the nephrogenesis mode found in <i>Mytilus</i> within the bivalves, and organogenesis in relation to delayed metamorphosis.</p>