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We employed landmark-based 3D geometric morphometrics to assess cranial size and shape diversification in Trichechus manatus and T. inunguis to compare it with patterns among all manatee taxa ( T. manatus latirostris, T. m. manatus, T. inunguis and T. senegalensis), and to analyse geographic variation within American manatee populations, using a sample of 189 skulls. Chromosome G- and C-banding techniques were performed in T. m. manatus from Brazil. All taxa were statistically discriminated by skull shape. Trichechus m. manatus and T. m. latirostris have larger skulls than T. inunguis. A morphological discontinuity was noted within T. m. manatus, with the Brazilian population south of the Amazon discriminated from the T. m. manatus Caribbean and T. m. latirostris USA populations. Specimens from Suriname and Guyana had a skull shape more similar to the one from the Caribbean population. The Brazil Antillean manatee population exhibited morphological differences similar in magnitude to those found between the Amazonian and African species. Additionally, structural chromosome differences were detected between that population (chromosome pair 4 is metacentric and 10 is submetacentric) and manatees from Puerto Rico and Florida. Based on such morphological discontinuity and chromosomal divergence, we hypothesize that the Amazon River mouth may be acting as a reproductive barrier for the T. m. manatus population in Brazil, thus indicating that its taxonomic status and conservation strategies need an urgent reassessment. [ABSTRACT FROM AUTHOR]