The official Star Trek Online website has been updated with a clarification on where exactly STO takes place in the Star Trek timeline. The new Star Trek movie changes things up a bit with the introduction of an alternate timeline, causing some potential complications.

In the update, Cryptic Studios assures their fans that Star Trek Online takes place during the "prime" reality, which includes all the previous Star Trek shows and the first 10 movies.
For more information on the timeline, go here.