Few studies have conducted morphological analyses of crocodilians, and little information exists on differences between size-classes and sexes in Neotropical crocodilians. In this study, we measured nine morphological traits in 121 captive Morelet's crocodiles Crocodylus moreletii (81 females and 40 males). Our results revealed that individuals < 2 m total length do not exhibit sexual dimorphism in morphometric characteristics. However, for crocodiles over 2 m in length, males were significantly larger than females in terms of dorsal-cranial length, cranial width, snout width and snout-ventral length. In general, morphological traits demonstrated a strongly significant relationship with total length at the smaller size class of 150–200 cm length. However, in the highest size class of 250–300 cm length (large adult males), morphological traits were no longer significantly related with total length. Male crocodiles demonstrated allometric growth of cranial morphology with significantly greater increase in cranial width, snout width, and mid-snout width relative to total length at higher size classes. Morphological dimorphism and allometric growth may be associated with adaptive strategies for reproductive success.