The Big Bang Theory star, who has sons Miles, 7, and Fred, 4, with Stone, cites "irreconcilable differences" for the split, which she revealed in a statement on her Kveller.com parenting blog.
"Divorce is terribly sad, painful and incomprehensible for children. It is not something we have decided lightly," she writes.
The former star of TV's Blossom, 36, also says that the split is not due to the attachment parenting she discusses in her book Beyond the Sling. "Relationships are complicated no matter what style of parenting you choose," she says.
"The main priority for us now is to make the transition to two loving homes as smooth and painless as possible," Bialik continues. "Our sons deserve parents committed to their growth and health and that’s what we are focusing on. Our privacy has always been important and is even more so now, and we thank you in advance for respecting it as we negotiate this new terrain."
She concludes by saying, "We will be ok."
The couple were married in August 2003 in Pasadena, Calif.