Pufferfish could be responsible for human intoxications due to the accumulation of lethal neurotoxin, called tetrodotoxin (TTX). While traditionally some species of pufferfish are consumed in Japan, their marketing is banned in the EU. In Israel, there is no legislation regarding the marketing of pufferfish. Moreover, as part of the Lessepsian migration phenomenon (migration of marine species across the Suez Canal), some species of the genus Lagocephalus have spread in the Mediterranean Sea during the last decades. These species may represent a significant emerging risk within the Israeli and other Mediterranean countries seafood chain. Taxonomic identification of marine organisms is sometimes hindered by morphological similarities and utilization of wrong criteria. Therefore, the morphological approach often requires the support of molecular tools which usually rely on a comparison of DNA sequences available in free publicly-accessible databases. This last process can be affected by incorrectly deposited sequences and lead to misidentifications of specimens’. This study aims to find a suitable molecular marker for quickly identifying Lagocephalus species in fresh and processed products. All available sequences of COI and cytb mitochondrial genes were used to create different length datasets (long and short fragments) to produce NJ trees depicting genetic relationships for Lagocephalus spp. The analysis of the proposed short fragment could represent a reliable food safety tool that prevents emerging risks associated to toxic Lagocephalus spp.