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Recent studies indicated that regeneration speed in caudal fin and kidney of the genus Aphaniusis faster than the other traditional model zebrafish. Therefore, non-traditional model organisms, such as members of the genus Aphanius, can probably be suitable candidate to study regeneration phenomenon. In order to advance our knowledge on the regeneration ability in the genus Aphanius, firstly we investigated the histology organization of caudal fin regeneration process in ten individuals of Aphanius hormuzensiswith 3.5–4.0 cm in total length. In addition, transcription of three controlling genes, i.e., the ligand (Eda) and the receptor (Edar) from ectodysplasin signaling pathway and mmp9 (matrix metallopeptidase 9), were examined during the caudal fin regeneration stages in Aphanius hormuzensis. For the later experiment, 55–60 fish specimens were used to obtain 50 mg tissue for each regeneration stages. Thereafter, the expression patterns of these genes were examined by quantitative real-time PCR. Our histological observations showed three distinct stages in caudal fin regeneration including a wound healing in 24 h post-amputation (hpa), the blastema formation in 72 hpa and the outgrowth with fin ray formation in 5 days post-amputation (dpa). The results of quantitative real-time PCR showed that mmp9 has a strong upregulation during the stages of blastema and fin ray formation. The Eda transcript level was significantly increased, and it has upregulation during the fin ray formation stage. Slight down-regulation of Edar transcripts was observed at the blastema stage, but it was upregulated thereafter. It is documented that ectodysplasin signaling has critical role in morphogenesis of ectodermal appendages, and mmp9 involves in the extracellular matrix remodeling during regeneration. As conclusion, Eda signaling is present and involve in different stages of the caudal fin regeneration in A. hormuzensis. Eda gene upregulation might support the hypothesis that the regulation of Eda/Edar signaling was controlled by the ligand (Eda) expression during the caudal fin regeneration of the studied killifish. Moreover, the upregulation of mmp9 in different stages of regeneration is consistent with its role in the removal of damaged cartilage matrix.