Deschanel confirmed to E! News she was expecting their first child together back in March, which of course, brought on speculation of whether or not Dr. Brennan would be expecting also.
The actress recently showed off her baby bump on the cover of Fit Pregnancy, where she said, "I really like being pregnant. I'm in awe of the process and the science. And seeing my belly move is pretty amazing; it's like in the movie Alien."
Now it's time for a whole new journey!
Her Bones costar T.J. Thyne celebrated via social media. "CONGRATULATIONS EMILY D!!!!!!!!!!!!!!" he tweeted Wednesday. "Yay yay yay!!! :o)"
But we're sure nothing will compare to Auntie Zooey Deschanel's excitement.