The DAPI (4′,6-diamidino-2-phenylindole) staining method is widely used to enumerate environmental bacteria. In this study, we provide evidence that the conventional DAPI method underestimates bacterial numbers under starvation conditions. In a study of bacteria from biofilms on decomposing maple leaves, treatment of cells with HCl increased the number of bacteria that were visible using DAPI. Laboratory experiments demonstrated induction of an underestimation of bacterial numbers using DAPI by placing a common stream bacterium, Burkholderia cepacia, in carbon limited medium. Although the mechanism by which HCl treatment caused increased visibility of cells is unknown, we suggest that production of DNA-binding, stress induced proteins may be responsible for the inability to stain some cells with DAPI.