American Airlines will only sell basic economy fares directly, not through traditional or online travel agencies. There are some cheaper fares that they reserve to their own channels as well. But generally speaking there are two sets of fares depending where outside of American Airlines that you book:

• Systems using ‘new distribution capability’ which helps American upsell ancillaries, like paid seat assignments, get access to the lowest fares
  
• Those systems that haven’t adopted this new system only get more expensive fares.

Here is Cranky Flier who analyzed the different American Airlines domestic fares now published through different channels.

Basic Economy…fares are no longer sold through traditional third party channels across the board..[Looking at the Phoenix market:]

…For flights under 1,000 miles, it seems American wants to be selling in the $170 range as a floor for traditional channels. If the lowest fare in the market is at that point of higher, then the price won’t vary by channel. But if the lowest fare is below that point, American will sell the low fare direct or using NDC but then increase to the $170 range for traditional channels.

Once you get over 1,000 miles, it jumps $50 to the $220 range where the same division is made. And over 2,000 miles, it jumps again to about $300 though that’s a small sample size. (Washington/National is just under 2,000 miles while Philly is over.) Lastly, we have Hawai’i in the $350 range.

American no longer sells discounted (R, I) first class fares through pure traditional channels, either.

In some markets, where American has to compete aggressively with other airlines, they are going to appear (in some cases much) more expensive than competitors. They want travel sellers to adopt the new paradigm and sell their ancillaries, and they’re willing to give up some sales in the process – hurting both themselves and potentially those travel sellers to get there.

Meanwhile, American “has entirely stopped selling fares on codeshares operated by JetBlue through traditional channels.” You can no longer buy a Boston – New York LaGuardia flight through a seller that isn’t using set up with New Distribution Capability. And JetBlue, which can’t technologically differentiate its fare distribution the way that American can, “has simply stopped selling fares that American only sells through NDC channels.” Their partnership just became less competitive. We are ironically awaiting a court decision in the federal government’s anti-trust case against the alliance.