The regeneration of paired appendages in certain fish and amphibian lineages is a well established and extensively studied regenerative phenomenon. The teleost fin is comprised of a proximal endoskeletal part (considered homologous to the Tetrapod limb) and a distal exoskeletal one, and these two parts form their bony elements through different ossification processes. In the past decade, a significant body of literature has been generated about the biology of exoskeletal regeneration in zebrafish. However, it is still not clear if this knowledge can be applied to the regeneration of endoskeletal parts. To address this question, we decided to compare endo- and exoskeletal regenerative capacity in zebrafish (Danio rerio) and mudskippers (Periophthalmus barbarous). In contrast to the reduced endoskeleton of zebrafish, Periophthalmus has well developed pectoral fins with a large and easily accessible endoskeleton. We performed exo- and endoskeletal amputations in both species and followed the regenerative processes. Unlike the almost flawless exoskeletal regeneration observed in zebrafish, regeneration following endoskeletal amputation is often impaired in this species. This difference is even more pronounced in Periophthalmus where we could observe no regeneration in endoskeletal structures. Therefore, regeneration is regulated differentially in the exo- and endoskeleton of teleost species.