The shrimp Macrobrachium amazonicum (Heller 1862) has an extremely large geographic range (>4000 km across) in northern and central South America, comprising estuarine and fully limnic inland populations, which are hydrologically isolated from each other. Significant variations in ecology, physiology, reproduction, and larval development suggest an at least incipient allopatric speciation due to limited genetic exchange. In a comparative experimental investigation with shrimps from the Pantanal (upper Paraguay River basin) and the Amazon delta, respectively, we measured larval body size, dry weight (W), biochemical (total protein; lipid; fatty acids, FA), and elemental composition (carbon, hydrogen, nitrogen; collectively CHN) at hatching. All these early larval traits are relevant for the degree of developmental dependence on planktonic food sources. Various consistent differences were observed between the two populations: Newly hatched larvae produced by shrimps from the Amazon delta were significantly smaller and showed lower values of W, CHN, protein, and unsaturated FA compared to those from the Pantanal. On the other hand, they contained significantly higher quantities of total lipid and saturated FA and, in consequence, higher ratios of lipid:protein, C:N, and saturated:unsaturated FA. All these differences in biomass and chemical composition suggest that the larvae of the Amazon population are energetically better adapted to planktonic food limitation, which likely occurs during riverine downstream transport toward coastal marine waters, also explaining previous observations of much stronger initial starvation tolerance in larvae from the Amazon versus those from the Pantanal. The latter develop in highly productive lentic inland waters, where large body size, an early onset of feeding, and a strong musculature (indicated by a high protein content) should facilitate their role as planktonic predators and allow for fast growth. An initial independence from food (lecithotrophy in the zoea I stage) as well as a preference for oligohaline rather than fully limnic conditions observed in the Pantanal larvae are interpreted as traits that have persisted from an ancestral coastal marine clade. Altogether, consistent ontogenetic differences between shrimps from the Pantanal and the Amazon estuary support the hypothesis that the taxon M. amazonicum comprises a complex of closely related but separate species.