The Scottish Fishermen's Federation (SFF) had taken a neutral stance before the 23 June referendum.
Members have now met in the wake of the result, and said Brexit was the preferred option.
The SFF is due to meet Fisheries Minister Fergus Ewing on Monday for talks about the way forward.
First Minister Nicola Sturgeon has said one of her priorities is to protect Scotland's place in the EU.
SFF chief executive Bertie Armstrong said the two standpoints seem to be incompatible.
He told BBC Scotland: "There is a gap between the two ambitions.
"For the fishing industry it's a complete no brainer - we should be out the EU and out the Common Fisheries Policy (CFP)."
A Scottish government spokesman said: "As the First Minister has stated, we are intent on pursuing all options to maintain Scotland's EU status.
"The first minister also made it clear during questions in parliament yesterday that she is aware of the feelings of the fishing industry and others who did not vote to remain.
"Although her priority continues to be the clear majority of people across Scotland who did vote to remain in the EU, she is keen for ministers to engage closely with the industry to listen to their concerns."
He added: "We are committed to ensuring Scotland's interests are at the heart of any EU decisions taken on fishing and ministers are continuously engaging in discussions with key stakeholders, this includes meeting with the Scottish Fishermen's Federation again on Monday."
The UK voted to leave the EU. The vote north of the border was to remain.
A flotilla of fishing boats sailed up the Thames to urge Parliament take back control of British waters last month.
The Scottish government said before the result that EU membership was in the "best interests" of Scotland's fishing industry.
In 2014, Scotland exported Â£449m of fish and seafood to Europe - 68% of the total value of Scottish food exports into that market.
Worldwide, seafood exports are the second largest food and drink export behind whisky, and the industry supports thousands of jobs.
The fishing industry wants out of the EU in the face of Scottish government efforts to keep the country in, ministers are being told.