The structural origin of the vertebrates’ paired limbs is still an unsolved problem. Historically, two hypotheses have been raised to explain the origin of vertebrate limbs: the Archipterygium Hypothesis and the Fin Fold Hypothesis. Current knowledge provides support for both ideas. In the recent years, it has been also suggested that (1) all appendages correspond to body axis duplications and (2) they are originated by the ventralization of the developmental program present in the median fins. The tail bud is also a relevant structure in the attempt to understand the origin of the vertebrates’ limbs. Due to their similarities in gene expression and general organization, both structures should be studied more closely to understand their potential evolutionary link. Interestingly, in non-vertebrate chordates such as Amphioxus, it is possible to find a tail fin that during development expresses several genes that are conserved with other vertebrates’ limbs and tails. This shared gene expression could be considered as an evidence of potential co-option of the same genetic tool kit from the tail to the extremities. This observation is congruent with the hypothesis of Axis paramorphism, which previously suggested similarities between the tail and limb buds.