An in situ hybridization technique with HNPP (2-hydroxy-3-naphthoic acid-2'-phenylanilide phosphate) and Fast Red TR was used to detect specific bacterial cells at the single-cell level. By this technique, the fluorescent signals of target bacterial cells were up to eight times more intense than those of standard fluorescence in situ hybridization with mono-fluorescein isothiocyanate-labeled oligonucleotide probes. This novel HNPP-Fast Red TR whole-cell hybridization technique is available for the identification of small or low-rRNA-content bacterial cells in the natural environment.