"They've always referred to them as their children, and it looks like Jen will keep the LA dogs with her and Justin will keep the pit bull in NYC," a source told the publication.
"But it was the biggest bone of contention in the split."
While the dogs may now be separated by thousands of miles, they won't have to say goodbye forever.
"They've made an arrangement for visitation," an insider said.
The Along Came Polly star became engaged to the Leftovers actor in August 2012, and they married in a surprise ceremony at their LA home on August 5, 2015.
While the separation is still somewhat fresh, it was claimed the pair had taken a crucial step to protect their multi-million dollar fortunes, with an 'iron-clad' pre-nup signed before their August 2015 wedding, reported US Weekly.
A source told the website: "Jennifer has an iron-clad prenup with Justin. It would be very hard for Justin to contest it. The prenup talks before the marriage were long and intense".