Non-native pufferfish have been a part of the Mediterranean marine ecosystem since the 1930s. However, there is a lack of knowledge regarding the by-catch of these species. This study aimed to compare the by-catch of pufferfish species between different types of fishing gear and to determine the monetary losses due to pufferfish on the Aegean (west) and Mediterranean (south) coasts of Turkey. A total of 467 commercial and recreational fishers (n= 244 and n=223 respectively), based in the 7 coastal cities were interviewed in the period of June - December 2017. A semi-structured questionnaire provided detailed information on by-catch amount of pufferfish in fishing gears, and economic loss caused by pufferfish. The most commonly caught pufferfish species was Lagocephalus sceleratus. The by-catch amount of pufferfish is higher on the Mediterranean coast in comparison with the Aegean coast. The highest pufferfish by-catch was recorded in purse seines and trawls on the south coasts, but in set nets on the west coasts. When seasonal changes were considered, the highest by-catch was occurred in the summer months for both commercial and recreational fisheries. Regarding the damages caused by pufferfish species in the small-scale fisheries, 92% and 90% of fishers, who fished on the south coasts, claimed that pufferfish species damage their fishing gears and fish entangled to these fishing gears, respectively. In conclusion, pufferfish species (e.g. L. sceleratus) are part of the ecosystem with their unknown quantified impacts. In fact, such information is required for fisheries management to mitigate the impacts of these species. The present study contributes to filling the gaps in this area.