Microalgae play a fundamental role in aquaculture systems, especially in nurseries. They can supplement the nutrition of cultured species, and also contribute to keep good water quality. Their value depends on the groups present in major abundance. Thus, being able to understand the factors that influence microalgae composition is key for an improved system management. In this study, the microalgae community structure in a Marsupenaeus japonicus nursery is studied. Instead of the classic microscopy approach, the composition and abundance of periphyton and phytoplankton were analyzed using signature pigments analysis by high pressure liquid chromatography coupled with the software CHEMTAX. The environmental parameters, which could affect periphyton and phytoplankton groups, were analyzed statistically. The results showed that diatoms were the dominant group both in phytoplankton and periphyton. The analysis of signature pigments, allowed to report the presence of previously undetected groups on periphyton, prasinophytes and prymnesiophytes, which are characterized by a high nutritional value. This is especially important in nurseries because of shrimp grazing on periphyton can increase post-larvae survival. Nutrients played a key role on phytoplankton development, but had a minor effect on periphyton, which was more affected by colonization processes and other environmental variables.