What alligator cracking actually is
Alligator cracking is a network of shallow, interconnected cracks that make your flat roof look like reptile skin or dried mud. It's one of the most common things homeowners spot on aging flat roofs.
Here's the good news up front: on most flat roofs, this is a surface problem. The top layer of coating or asphalt has dried out and gone brittle, and daily heating and cooling has cracked that stiff skin.
The layers underneath (the felts, the membrane, the deck) are often still doing their job. That's why an alligatored roof can look alarming and still be watertight.
The whole game is timing. Recoat while the cracks are tight and shallow, and you add years for about the price of a nice dinner out. Wait until water finds a way through, and the number climbs fast.
Why your flat roof is alligatoring
The number one cause is plain aging from the sun. UV light and heat bake the oils out of asphalt and coatings over 10 to 20 years. Once those oils are gone, the surface can't flex with the daily temperature swing, so it cracks.
If your roof has an old silver aluminum coating, that's often what you're seeing crack. Those coatings only last 3 to 7 years, and they craze on the surface while the roof under them stays fine.
Sometimes the cause is a bad coating job. If a coating went on too thick, or in cold or humid weather, it skins over on top before it cures underneath. That uneven cure cracks early, sometimes within a year or two.
Ponding water makes everything worse in the low spots. Areas that hold water after rain age faster, so you'll often see the worst alligatoring near drains and in corners that don't drain well.
The one cause you don't want is a membrane that's simply reached the end. If the roof is over 20 years old and the cracking comes with soft spots, blisters, and failing seams, no coating will save it.