1, 2, 5, 6, 9, 10-Hexabromocyclododecanes (HBCDs) are new brominated flame retardants causing serious environmental pollution. Dozens of degradative bacteria have been found with capacity to transform HBCDs. In the present study, an aerobic functional bacterium Rhodococcus strain stu-38 was isolated from enriched culture of mangrove sediment using HBCDs as carbon source. This strain could stereoselectively transform HBCDs, the removal rate was α->γ->β-HBCD in the mineral salt medium, but was β->α- and γ-HBCD in the growth medium, and it selectively transformed γ- HBCD in the seawater. Transformation rate of strain stu-38 was lower than other functional strains, however, seven potential debrominated products of HBCDs were identified by using GC-MS. These debrominated products, included dibromocyclododecadiene, bromocyclododecadienol and bromocyclododecatriene were formed through reductive debromination, hydrolytic debromination and dehydrobromination. Overall, Rhodococcus sp. stu-38 diastereoisomer-specifically transformed HBCDs to various debrominated products in the different cultural media, which highlighted the complicated stereoselective biotransformation of HBCDs.