Changes in amino acid composition (AAC) during ontogeny of some planktonic crustacean species commonly found in fresh and brackish coastal waters were compared. For these comparisons two calanoid copepods (Eurytemora velox and Calanipeda aquae-dulcis), two cyclopoid copepods (Diacyclops bicuspidatus odessanus and Acanthocyclops robustus) and two Daphnia (Daphnia pulicaria and Daphnia magna) species were selected. A discriminant analysis was performed to determine whether there were significant differences between the AAC of the different stages of each species. Results show gradual changes in AAC during ontogeny of the copepod species. Calanoids showed the greatest differences in AAC between stages, followed by cyclopoids. Gradual changes in AAC were due to the increase in some amino acids such as alanine, valine, glutamic acid, glycine, arginine, proline and tyrosine from nauplii to adults. The latter showed a remarkable increase in all copepod species. In contrast, Daphnia species showed a relatively constant AAC during development, with only minor changes being detected, and not related with ontogeny. Differences in the physico-chemical variables of the lagoons do not seem to be the cause of copepod ontogenic changes in AAC. Data suggest that AAC differences found between stages of copepod species could indicate a gradual change in diet during the life cycle of these copepods.