Gene, who made more than 170 appearances for the Robins as a player, combined his assistant coach role at the KC Lightstream Stadium with head coach duties with Championship One side Thunder in 2014.
New Rovers head coach Chris Chester has opted to bring in his own staff for next season, resulting in Gene’s departure.
Gene said: “I’m disappointed that I won’t be staying at Rovers, a club that means a lot to me, but I wish everybody here all the best for next season.
“I had a chat with Chezzy when he took over about what he had in mind for next year and he was up front about wanting to bring his own people in. It was tough to take at first but I understand his reasons why.
“I’ve learned a lot over the past three years and I’m grateful to Hull KR for giving me an opportunity to come back to the club after my playing days finished. I love the club and the fans and I leave with some great memories. I’ll be in the stands supporting the team as often as I can next season and who knows, maybe I’ll be back here as a coach one day.
“You have to move on in life and I’m excited about taking on a bigger role at Gateshead. I’m really proud of what the team achieved this season and my focus now is on having another good year in 2015.”
Chief executive Mike Smith said: “Stan is a true Rovers legend and he has done a terrific job on the coaching staff, but Chris Chester wants to appoint his own backroom staff and Stan understands that.
“He has done a great job up at Gateshead this season and our young players have really developed under the dual registration system. I’ve no doubt the Thunder will continue to improve under Stan’s leadership and having him there will strengthen the partnership between the two clubs even further.”