Wetland tree species are of importance for economic and restoration purposes. We describe the germination process and seedling morphology of six arboreal native species typical of Southeastern Mexico: Annona glabra, Ceiba pentandra, Pachira aquatica, Haematoxylum campechianum, Coccoloba barbadensis and Crataeva tapia. A total of 300 seeds per species were planted in a mixture of sand, cocoa plant husk and black soil (1:1:1), and maintained in a tree nursery with 30% artificial shade, from February to November of 2007. We carried out the morphological characterization, and elaborated a key to seedlings based on: 1) germination type 2) seedling axis and 3) leaf elements. P. aquatica has cryptocotylar hypogeal germination, the others have phanerocotylar epigeal germination. Germination rates were high (>86%), except for C. barbadensis (69%).