Skull morphological characters are used for species and subspecies identification in the manatees, but no comparative study has investigated skull growth. We examined progressive ossification in the cranial sutures of 251 skulls of West Indian manatees, 19 skulls of African manatees and 17 skulls of Amazonian manatees. Degrees of cranial suture fusion were evaluated based on gross observations of skull specimens. Our results suggest that ossification patterns in occipital region sutures follow a fixed sequence in living manatees. In all manatees, the suture between the sphenoid and occipital bones fused first, while the supraoccipital-exoccipital synchondrosis fused last. The ossification sequence observed in manatees was not found in descriptions of other mammals, including the dugong. We concluded that this ossification sequence is a unique, common character of living manatees. We also found two differences in the sequence of occipital region development in two subspecies of the West Indian manatee. The shape of the Foramen magnum is considered to be an important character for the classification of the two subspecies of the West Indian manatee. The different ossification sequences detected in this study are probably reflected in the different shapes of the Foramen magnum.