10/18/13 Thanks to reader Rebecca for nudging me (see the comments below) to update this post. Since I wrote it, Southwest and AirTran have snuggled into a cozier embrace and now you can bring a pet on a “shared itinerary” (that is, travel plans that include flight legs on Southwest and AirTran planes). However, you can only make advanced reservations for your in-cabin pet on non-shared, AirTran-only itineraries. If you fly entirely on AirTran flights, “Advanced reservations must be made by calling AirTran Airways at 1-800-AIR-TRAN (1-800-247-8726), and the Pet Fare payment will be required at that time.” Southwest’s pet page is currently poorly written, and speaks only about shared itineraries, but I am confident that its usual first-come-first-served policy still applies to Southwest-only itineraries.

If you are traveling with a pet, be sure that your itinerary includes only flights on one carrier or the other (and if you plan to travel on AirTran only, book your travel through AirTran, not Southwest). This issue arose many months ago, shortly after the merger between Southwest and AirTran started taking practical effect. I held off posting about it, partly because my to-do list has taken on a life of its own, but largely because I thought the problem wouldn’t last long. That appears not to be the case.

So why is this an issue? Haven’t the airlines, well, merged? Yes, but complete integration takes time. AirTran’s website explains that “Though AirTran Airways is a wholly-owned subsidiary of Southwest Airlines, the two are still operating as separate carriers.” They apparently anticipate being fully integrated by the end of 2014. In the meantime, you will be be allowed to travel with a pet on “shared itineraries,” i.e., either (1) a travel plan that includes both Southwest and AirTran flights, or (2) a travel plan consisting of AirTran-only flights that you’ve booked through Southwest’s site.

In neither of those cases will you be allowed to add a pet to your reservation, per Southwest’s website:

“Shared itineraries or AirTran-only itineraries booked through Southwest channels cannot be purchased for Pets, Unaccompanied Minors, or Groups. Please note that you cannot add a pet to a shared itinerary over the phone, nor can you add a pet to a shared itinerary upon arrival at the airport. Pets are not permitted to travel on shared itineraries.”

Earlier this year, a Dog Jaunt reader found herself in trouble when she purchased an itinerary on-line that included both Southwest and AirTran flights — when she called to add her pet to her reservations, she learned she couldn’t. She managed to get herself an all-Southwest booking, but I’ve no doubt her blood pressure suffered.

The two entities have similar pet policies in some respects (neither accepts checked pets, and both charge a $75 fee). They also both regard a pet carrier as a replacement for either your carry-on or your personal item, which is a big benefit to people who prefer not to check luggage. One difference is that Southwest tells travelers what space is available under their seats, while AirTran specifies a maximum carrier size. Another is that AirTran permits only one pet per traveler, and Southwest will let up to two pets share a carrier.

An important difference to note between Southwest and AirTran is that despite a preamble that suggests otherwise (“Reservations for small cats and dogs can only be booked by calling Southwest Airlines at 1-800-I-FLY-SWA”), Southwest does not in fact reserve a spot on the plane for your pet: The very next sentence reads “Pets will be accepted on a first-come, first-served basis until capacity is reached.” AirTran, by contrast, will reserve your pet a spot: “As limited space is available, advanced reservations must be made.” [10/18/13 As I’ve tried to indicate with my strike-throughs, Southwest has edited its pet policy to remove the misleading “reservations” language — now they’re quite clear that “Pets will be accepted on a first-come, first-served basis until capacity is reached.”]

We travel a great deal on Southwest, and to date their policy has not caused us trouble — five pets per flight are allowed, and we have not yet been in a situation where six pets showed up. It does take one worry off your mind, however, to know that your pet has an in-cabin space waiting for her; we appreciate the airlines that accept reservations for in-cabin pets, and I hope that Southwest adopts AirTran’s policy when the integration process is complete.