Histamine is a neurotransmitter crucial to the visual processing of Drosophila melanogaster. It is inactivated by metabolism to carcinine, a β-alanyl derivative, and the same enzyme that controls that process also converts dopamine to N-β-alanyl dopamine. Direct detection of histamine and carcinine has not been reported in single Drosophila brains. Here we quantify histamine, carcinine, dopamine, and N-β-alanyl dopamine in Drosophila tissues by capillary electrophoresis coupled to fast-scan cyclic voltammetry (CE-FSCV). Limits of detection were low, 4 ± 1 pg for histamine, 10 ± 4 pg for carcinine, 2.8 ± 0.3 pg for dopamine, and 9 ± 3 pg for N-β-alanyl-dopamine. Tissue content was compared in the brain, eyes, and cuticle from wild type (Canton S) and mutant (tan3 and ebony1) strains. In tan3 mutants, the enzyme that produces histamine from carcinine is non-functional while in ebony1 mutants, the enzyme that produces carcinine from histamine is non-functional. In all fly strains, the neurotransmitter content was highest in the eyes and there were no strain differences for tissue content in the cuticle. The main finding was that carcinine levels changed significantly in the mutant flies while histamine levels did not. In particular, tan3 flies had significantly higher carcinine levels in the eyes and brain than Canton S or ebony1 flies. N-β-alanyl-dopamine was detected in tan3 mutants, but not in other strains. These results show the utility of CE-FSCV for sensitive detection of histamine and carcinine which allows a better understanding of their content and metabolism in different types of tissues.