While the production of polybrominated diphenyl ethers (PBDEs) was gradually phased out in the last decade, they may still pose hidden danger to the environment due to their toxicity and persistence. On the other hand, alternative halogenated flame retardants (AHFRs) have been increasingly used as substitutes for PBDEs and may further worsen environmental health. To determine the environmental impact of PBDEs and AHFRs, we examined the historical trends and ecological risks of PBDEs and AHFRs in a typical industrialized city in South China by measuring their concentrations in mangrove sediment. Results showed that the concentrations of PBDEs increased abruptly from 1997 to 2009 due to the use of commercial deca-BDE mixture, but were stabilized in recent years. The concentrations of AHFRs, mainly contributed by decabromodiphenyl ethane (DBDPE), kept increasing from 1997 onwards. Based on the temporal trends, DBDPE is predicted to be predominant over BDE 209 in future. Despite the observed similar concentration between BDE 209 and DBDPE, the former posed a high ecological risk, while the ecological risk of the latter was negligible. Therefore, more attention is required to manage the contamination of BDE 209 in the environment.