Histamine has been shown to modulate visual system and photic behavior in arthropods. However, few methods are available for the direct quantification of histamine and its precursor and metabolites in arthropod brain. In this work, a method for the separation of histamine, its precursor histidine, and its metabolite N-methyl-histamine from brain extracts of a freshwater crustacean has been developed using capillary electrophoresis with laser-induced fluorescence detection. Molecules were tagged on their primary amine function with naphthalene-2,3-dicarboxaldehyde, but derivatized histamine and N-methyl-histamine exhibited poor stability in contrast to derivatized histidine. To overcome this limitation, an automated derivatization performed within the capillary electrophoresis instrument was optimized and quantitatively validated. The limits of detection were 50, 30, and 60 nmol/L for histidine, histamine, and N-methyl-histamine, respectively. This study reports, for the first time, the amounts of histamine and its related compounds in brain extracts from populations of the freshwater amphipod Gammarus fossarum, and shows that these amounts vary mainly according to population and season, but are not affected by an experimental electrical shock.