Mr Pye has informed the board of the Sheffield-based aquaculture health, nutrition and genetics business that he wishes to step down to allow the company to appoint a new leader to drive the next phase of Benchmark's growth and development.
Peter George, chairman of Benchmark, will step up, with immediate effect, to executive chairman and will remain in this role through to the appointment of a new CEO, something the firm said would "ensure a smooth transition period and a successful handover of Malcolm's role and responsibilities".
Mr Pye has been with the group since its foundation. He was part of the team that saw it listed on the AIM and oversaw an acquisitive and organic growth. Today the firm employs mor than 1,000 people and operates in 27 countries.
However recent results for Benchmark have shown it to be struggling. The firm's last results showed pre-tax profits had slumped 80 per cent and Mr Pye's departure comes hot on the heels of the departure of chief financial officer Mark Plampin who stepped down last month.
The company said it has already commenced an external search for a successor and a further announcement will be made in due course.
"We are delighted that he will remain with Benchmark in a NED role, which will ensure we retain his significant expertise.
"I joined Benchmark because I loved Malcolm's passion for the business and sector; he has been instrumental in developing a culture in the business that is passionate about sustainability and animal welfare, and we are committed to building on that process.
"We have begun the search for his successor and look forward to updating on progress and ensuring a smooth handover of duties in due course."