The exceptional regenerative capacities of the Mexican axolotl (Ambystoma mexicanum) have made it one of the most prominent organisms in the study of vertebrate regeneration. Here we present results of a genomic survey of small RNAs during limb regeneration using 454 high‐throughput sequencing technology. We mapped small RNAs to an axolotl transcriptome assembly and to a representative library of repetitive DNA sequences sampled from the axolotl genome. Intriguingly, the majority of the axolotl small RNAs (~72%) mapped to repetitive DNA elements while only ~8% corresponded to microRNAs. We identified several microRNAs which appear to be regulated over the regeneration time‐course, several of which are conserved in a zebrafish fin regeneration model. We identified unusual small RNAs that emerge during the regenerative process which could be endogenous siRNAs or piRNAs; several of these were successfully mapped to assembled, protein‐coding transcripts. These observations suggest a small‐RNA mediated mechanism for regeneration that is conserved in vertebrates which employs small RNA classes which have been previously ascribed to pluripotent cell types.