If your pets will fit in a carrier and fit on a bus seat you can buy tickets on express bus for them to have seats, I have done this a few times in Belize, not Mexico. You will get some stink eye from passengers but hold your own, you have purchased seats. This wont work on regular buses. Morales transfer is also a good choice. Or you could take a water taxi to San Pedro, then to Chetumal, San Pedro Express has dog crates of all sizes. You may be able to rent a car in Chetumal.

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