Histamine is a fermented food product that exerts adverse health effects on animals when consumed in high amounts. This biogenic amine is fermented by microorganisms from histidine through the activity of histidine decarboxylase. Drosophila melanogaster can discriminate histidine and histamine using GR22e and IR76b in bitter-sensing gustatory receptor neurons (GRNs). In this study, RNA interference screens were conducted to examine 28 uncharacterized gustatory receptor genes using electrophysiology and behavioral experiments, including the binary food choice and proboscis extension response assays. GR9a and GR98a were first identified as specific histamine receptors by evaluating newly generated null mutants and recovery experiments by expressing their wild-type cDNA in the bitter-sensing GRNs. We further determined that histamine sensation was mainly mediated by the labellum but not by the legs, as demonstrated by the proboscis extension response assay. Our findings indicated that toxic histamine directly activates bitter-sensing GRNs in S-type sensilla, and this response is mediated by the GR9a, GR22e, and GR98a gustatory receptors.