Phytoremediation is a novel treatment option for weathered, hydrocarbon contaminated, flare-pit soil in prairie ecosystems. The remediation potential of six different naturalized prairie plants was assessed by examining their impact on the degradation potential of indigenous bacterial communities. Culture-based and culture-independent microbiological methods were used to determine if mixed plant treatments stimulate different microbial communities and catabolic genotypes in comparison to individual plant species that comprise the mix. DGGE analysis of PCR-amplified 16S rRNA genes revealed that alfalfa (Medicago sativa) had a dominant effect on the structure of rhizosphere microbial communities in mixed plant treatments, stimulating relative increases in specific Bacteroidetes and Proteobacteria populations. Alfalfa and mixes containing alfalfa, while supporting 100 times more culturable PAH degraders than other treatments, exhibited only 10% TPH reduction, less than all planted treatments except perennial rye grass (Lolium perenne). Total petroleum hydrocarbon (TPH) reduction was greatest in single-species grass treatments, with creeping red fescue (Festuca rubra) reducing the TPH concentration by 50% after 4.5 months. Overall TPH reduction throughout the study was positively correlated ( p < 0.001 ) to culturable n-hexadecane degraders.