Novel 16S-rRNA targeted oligonucleotide probes (FW_iso_62 and FW_iso_761) were designed to detect Bordetella sp. by fluorescence in situ hybridization (FISH). Strong fluorescence signals with the probes were observed in 20% ~ 60% formamide concentrations. Quantification of Bordetella sp. in soil was developed with the selected probe of FW_iso_62 and its competitor combined with Nycodenz and DAPI technique. The advantages of the established DAPI_FISH: eliminate autofluorescence of soil particles masking the bacterial signals; ensure a large amount of bacteria in one picture for reliable statistical analysis; and keep efficiently in situ information of the bacteria 1,2,4-trichlorobenzene degrading. Bordetella bacteria were investigated in soils with the established method. The Bordetella bacterium was not detected in the agricultural soil, which was not exposed to chlorobenzenes. On the contrary, a lot of Bordetella bacteria (3.78×10⁶ cell g^-1) were determined in the soil contaminated with chlorobenzenes. When the 1,2,4-TCB-degrading Bordetella strain and its community in the contaminated soil were re-inoculated into the agricultural soil, the Bordetella numbers increased and accounted for 1.7％ and 3.8％ of the DAPI counts after incubation for 1 month, respectively. The probes developed in this study are useful for detecting Bordetella bacteria in complicated environmental samples.