Phagocytes are cells that pursue, engulf, and kill bacteria. They include macrophages and neutrophils of the mammalian immune system, but also free-living amoebae that hunt and engulf bacteria for food. Phagocytosis can result in diverse outcomes, ranging from sustenance to infection and colonization by either pathogens or beneficial symbionts—and thus, discrimination may be necessary to seek out good bacteria while avoiding bad ones. Here we tested whether the soil amoeba Dictyostelium discoideum can discriminate among different types of bacteria, using behavioral assays where amoebae were presented with paired choices of different bacteria. We observed variation in the extent to which the amoebae pursued different types of bacteria, as well as preferential migration towards Gram-negative over Gram-positive bacteria. Response profiles were similar for amoebae that originated from different geographic locations, suggesting that chase preference is conserved across much of the species range. While prior work has demonstrated that bacteria will use chemotaxis to seek out amoebae they colonize, our work suggests that the opposite also occurs—amoebae can preferentially direct themselves to particular bacteria in the environment. Preferential sensing and response may help to explain why some amoeba-bacterial associations are more common in nature than others.