Such itineraries previously had not been possible on Southwest and AirTran, even though the airlines' merger closed in the spring of 2011.
Southwest says it began testing linking itineraries with AirTran in a five-city "initial phase" that began Jan. 26. Southwest dubbed that test—which focused Atlanta, Fort Lauderdale, Fort Myers, Louisville and Norfolk—a success, saying it's now ready for a broad expansion of the effort.
Southwest will roll out the next phase on February 25, when it and AirTran will connect their flights options in 39 more cities. Southwest adds it's "on pace" to fully connect the airlines' combined 97 destinations, including international, by the end of April. (Read more: More Destinations as Southwest, AirTran Blend Frequent Flier Perks)
"Connecting the networks is a priority in 2013 and a major milestone as we work to combine our two Companies," Bob Jordan, Chief Commercial Officer at Southwest Airlines and President of AirTran, said in a statement. "With a connected network, we can offer Customers more itineraries, more destinations, more low fares, and a taste of what's to come once the integration is complete."
It also will allow Southwest to begin reaping some of the benefits it envisioned when it engineered its merger with AirTran.
Eventually, AirTran's brand will disappear as Southwest assimilates its operations into its own—but that's not expected to be complete until 2015.
Prior to January's tentative effort to link flights, Southwest had been limited in its ability to capitalize on the merger by funneling AirTran passengers—and destinations—into its own network.
Even with the linked flights, one area will remain murky for the airlines' customers: fees. (Read more: Southwest Airlines Adds $40 Fee for Early Boarding)
Most notably, Southwest allows customers two checked bags at no change. AirTran charges a fee.
So, how will the carriers sort that out for their linked flights?
Southwest says customers will get Southwest's checked-baggage allowance on any itinerary that involves a Southwest flight. For other fees, however, Southwest says it will enforce the fee policy of the airline through which the ticket is booked.