In-situ realtime method that can monitor the target bacteria should be used to determine the real situation of the bacteria in deep parts of heaps in heap bioleaching plants. This study suggest to apply flow cytometry technology to in-situ realtime monitoring of target bacteria. Flow cytometry is a method that can rapidly quantify the bacterial cells in bacterial suspension based on the detection of lights that are emitted from bacterial cells. In this study, we estimated the possibility of the application of flow cytometry to the selective detection of target bacteria. The bacterial culture solution that had been diluted by water including other bacteria was provided for fluorescence spectral analysis and scattered light analysis that were functions of flow cytometry. Our target bacteria could be selectively detected by those analyses in this study, therefore, it was shown that the flow cytometry could be useful for detecting target bacteria selectively. Because the measurement principle of flow cytometry is quite simple, it can be expected to be installed into deep heaps through the monitoring wells and determine the dominance of target bacteria in-situ and realtime in the future.