Birdsall will take up the role of strength and conditioning coach with Dougie Freedman's men and his former boss, Jim Bentley, had nothing but praise following his departure from the Globe Arena.
"We are obviously very sorry to lose Danny because he has done an amazing job for us over the years," the Shrimps boss told morecambefc.com.
"If you look at our records over the past couple of seasons you will see that we have had very few muscle injuries and that is testament to the work he has done.
"It is a dream move for him and he certainly goes with our best wishes and I am sure he will do a great job for Bolton."
The search for Birdsall's replacement has already begun and the League Two club hope to make an announcement shortly.