The accurate determination of bisphosphonate levels in bone and biological fluids is important in both clinical and pharmacological/toxicological studies; however, the quantitative analysis of the bisphosphonate is difficult because its concentration is quite low in most of biological sample. A novel fluorescent chemosensor (FCS)-based measurement method of bisphosphaonate levels using Naphta-diDPA-$2Zn^{2+}$ (NadDPA-$2Zn^{2+}$, DPA = dipycolylamine), an excellent FCS previously used for detecting PPi, was developed. By the FCS method, the concentration of bisphosphonates having no fluorophores can be determined analyzed with sufficient sensitivity. The results of this study indicate that the FCS-based measurement can be a useful method to analyze bisphosphonates in biological samples.