A source tells ET that the split was actually a long time coming, and that one of the major factors that played into their break-up was a fundamental disagreement about where the couple should live.
According to ET's source, Theroux thoroughly considers himself to be a New Yorker, and living in Hollywood was something that he never really wanted.
"He much prefers being [in New York] and that's been a major issue for them for a long time," says the source. Adding, that the actor's roots are deep in the Big Apple, and that his friends and social group, which Theroux holds close to his heart, are all based in the city.
“Justin has a very diverse friend group, and he likes that they're not all 'in the industry,'" says the source. "He's friends with people in the restaurant world, writers, comedians, artists, tattoo artists. It's an eclectic group and he doesn't have that type of network in LA."
The source said that Aniston, however, does not feel the same way about New York -- despite growing up as a kid and developing her early career there.
Additionally, the two stars' experiences with life in New York were vastly different. "Justin can hop on his [motorcycle], walk in the neighborhood, hang at a bar and all that without being bothered, but for Jen, the paparazzi are all over her," the source noted.
“He really wanted her to be comfortable [in New York]," the source says, explaining how Theroux tried hard to make his wife come to love the city. "He even negotiated with the paps to make a deal that they would only shoot her once per day and then leave her alone. He also agreed to move out of his apartment, which he loves."
In an attempt to give New York a shot, the source says the couple moved into an apartment in the West Village. However, there were some drawbacks that became immediately apparent. Aside from the fact that there was no garage, the presence of a small public park across the street provided a prime location for paparazzi to set up shop waiting to snap of pic of the former Friends star coming and going from her home.
The presence of unwanted tabloid attention also drew the ire of the couple's neighbors.
"There was the construction, which is obviously a nuisance, but what really pissed off the neighbors was just the constant commotion outside their door all the time with the photographers," the source says. "It made for an awkward living situation for Jen and Justin because they knew the neighbors weren't happy."
The tension came to a head in what the source refers to as "the bologna incident," in which Theroux came downstairs to discover that someone had covered his motorcycle in slices of bologna, and Aniston believed it was one of their neighbors who did it.
"She just never really could get settled in, she wasn't happy [in New York]," according to the source.
While the couple ended up selling their apartment in the West Village, the source says Theroux never gave up his apartment in Greenwich Village and he would stay there whenever he had to return to the city for work. However, Aniston rarely would stay there with him and often opted to stay at luxury hotels instead.
"She rarely stayed at his place, she preferred hotels," says the source. Adding, "Justin, on the other hand, did not like staying at hotels -- especially uptown. He eventually convinced her to at least stay in hotels with him downtown, like the Bowery hotel."
Despite their differences when it came where they wanted to live and their eventual split, the source stressed that the two really did love each other, and doesn't believe that there was any one incident that tore them apart. Rather, the wedge was slowly driven between them by their very different lifestyles, and it became a bigger problem over the course of their relationship.
"They really were a great couple. And they cared a lot about each other. Justin was always really protective of her," says the source. "They both wanted this to work."
"In an effort to reduce any further speculation, we have decided to announce our separation," Aniston and Theroux's statement reads. "This decision was mutual and lovingly made at the end of last year. We are two best friends who have decided to part ways as a couple, but look forward to continuing our cherished friendship."
"Normally we would do this privately, but given that the gossip industry cannot resist an opportunity to speculate and invent, we wanted to convey the truth directly. Whatever else is printed about us that is not directly from us, is someone else’s fictional narrative," the statement continues. "Above all, we are determined to maintain the deep respect and love that we have for one another."