Colonies of the red harvester ant, Pogonomyrmex barbatus, regulate foraging activity based on food availability and local conditions. Colony variation in foraging behavior is thought to be linked to biogenic amine signaling and metabolism. Measurements of differences in neurotransmitters have not been made among ant colonies in a natural environment. Here, for the first time, we quantified tissue content of 4 biogenic amines (dopamine, serotonin, octopamine, and tyramine) in single forager brains from 9 red harvester ant colonies collected in the field. Capillary electrophoresis coupled with fast-scan cyclic voltammetry (CE-FSCV) was used to separate and detect the amines in individual ant brains. Low levels of biogenic amines were detected using field-amplified sample stacking by preparing a single brain tissue sample in acetonitrile and perchloric acid. The method provides low detection limits: 1 nM for dopamine, 2 nM for serotonin, 5 nM for octopamine, and 4 nM for tyramine. Overall, the content of dopamine (47 ± 9 pg/brain) was highest, followed by octopamine (36 ± 10 pg/brain), serotonin (20 ± 4 pg/brain), and tyramine (14 ± 3 pg/brain). Relative standard deviations were high, but there was less variation within a colony than among colonies, so the neurotransmitter content of each colony might change with environmental conditions. This study demonstrates that CE-FSCV is a useful method for investigating natural variation in neurotransmitter content in single ant brains and could be useful for future studies correlating tissue content with colony behavior such as foraging. Graphical abstract.