Applying genome-wide computational-based approaches (using the draft genome sequence published in recent years) and following a set of strict filtering criteria, a total of 48 potentially conserved microRNAs belonging to 30 families were identified from economically important fish tuna (Thunnus orientalis). Using BLAST and RNA hybrid program a total of 19 potential miRNA targets were also identified in this study, which includes a number of signaling molecules (serine/threonine-protein kinase, GTPase activating protein etc.) and transcription factors (F-box protein, zinc finger protein etc.). This study provides the basis for gaining a better understanding of miRNA-mediated gene regulatory processes in fishes.