Unless you stay strictly on the most beaten of beaten paths in the Yucatan, you are almost sure to encounter some interesting animals and birds.
Birds are the easiest, and sometimes the most spectacular. The motmot is a large, very beautiful bird with iridescent blue-green feathers and a long tail. It's almost surprising that such a remarkable bird would be common, but we saw several each day.
Parrots are a frequent sight, chattering in the trees overhead. Tanagers make brilliant spots of color in the forests.
Toucans are somewhat rarer; we spotted them three or four times over the course of our ten days in the Yucatan. We had our best toucan-spotting luck in the less-touristy biosphere reserves on the eastern side of the peninsula.
There are also turkey-like birds whose names I never learned, vultures, and the occasional hawk. I'm told that there are hummingbirds, but I never saw one.
Flamingoes are very dramatic in the wild. From a distance, they're a low, sunset-like strip of pink on the blue horizon of the water; close up, they're a constant honking, stirring mass of salmon-colored feathers, set off by dramatic black bills and wing stripes. If they're alarmed, they stilt off through the water at a hilarious run -- though of course you should try not to scare them if possible.
The way to see flamingoes is to rent a boat at Celestùn on the northwest tip of the peninsula, about an hour and a half's drive from Merida. This isn't cheap: $40 for a one-hour trip to the flamingoes, $80 for a three-hour trip which includes a larger tour of the estuary and a wider array of bird life. But boats will seat up to 10 people, and since they depart from a central location (just after a bridge on the only road into Celestùn), you can wait around for other small groups to team up with to split the costs.
Naturally, there are a lot of other shore birds too: brown pelicans, big heavy birds which glide over the water with their wattles wagging, looking jealously at the much prettier, more agile terns; several kinds of herons; kingfishers like sapphires; pristine egrets; and myriads of gulls.
Mammals are harder to spot, but they're there, too. We never saw a jaguar, but we did see an armadillo and -- lurking on a garbage pile -- a coatimundi, a great, red, hairy animal almost the size of a golden retriever, with a snout a little like an anteater's and very surprised eyes.
With the exception of the shore birds, all these creatures were in the biosphere reserves surrounding major Mayan ruins. The best time for animal-watching is dawn or dusk; we found that the sites' closing times tended to coincide with the first fading of the light. The pyramids tend to be a long way from the entrance gates; this meant that we saw most of our animals on the walk back through the woods at the end of the day's pyramid-climbing. Even without armadillos, these end-of-the-day walks were lovely, accompanied as they were by frogs and crickets starting to hum in the dusky woods and the rustle of birds in the undergrowth.