The popular centre-half, 35, has made more than 300 appearances in two spells with the Shrimpers and helped them to promotion from League Two last season.
He said: “I’m delighted and really pleased to put pen to paper for another year. I’m looking forward to next year already.
“It’s great to know where I’ll be next season. I have a lot to offer still and I’m still hungry for success. I’m over the moon.
“I had other offers but this was the only place I wanted to be. I want to play a big part next season.”