Ciprofloxacin (CIP) is one of most used quinolone antibiotics detected frequently in agricultural soils and vegetables. In the present study, variations in microbial community and CIP removal in rhizospheric soils between two cultivars of Brassica parachinensis L. that accumulate higher and lower CIP (Sijiu and Cutai, respectively) were investigated under CIP stress (0mg/kg in CK, 2.94mg/kg in T1, and 67.11mg/kg in T2). The removal rates of CIP in rhizospheric soils of cultivar Sijiu were higher than those of cultivar Cutai, with a significant difference in T2 (48.7%>39.4%, P<0.05). The pyrosequencing of 16S rRNA and ITS gene indicated that the microbial diversity and community structure in rhizospheric soils of the two cultivars varied significantly. Spirochaeta and Trichosporon might be associated with CIP degradation, and higher relative abundances of Trichosporon in rhizoshperic soils of cultivar Sijiu might be responsible for higher CIP removal. Fourteen bacterial genera and ten fungal genera were screened as potential biomarkers for CIP removal process. The community level physiological profiling in rhizospheric soils of the two cultivars under CIP stress differed significantly, and more C substrates that favored CIP removal were observed in rhizoshperic soils of cultivar Sijiu. Our results demonstrate that variations in microbial community and the utilization of C substrates played important roles in differring the CIP removal in rhizospheric soils between the two cultivars.