As the use of certain brominated flame retardants (BFRs) has been globally banned due to their high toxicity to biota, organophosphate flame retardants (OPFRs) have been proposed as alternatives. Currently, OPFRs are ubiquitously found in the ocean at levels comparable to those of BFRs; however, information on the comparative toxicities of BFRs and OPFRs to marine biota remains limited. In this study, we investigated the toxic effects of aryl and halogenatedOPFRs, triphenyl phosphate (TPhP) and tris(1,3-dichloro-2-propyl) phosphate (TDCPP), on the brackish water flea Diaphanosoma celebensis at the in vivo and molecular levels and compared them with those of a typical BFR, hexabromocyclododecane (HBCDD). Moreover, we investigated the effects of TPhP on transcriptomic modulation to understand the underlying mechanisms of toxicity. The results showed that all three FRs negatively affected reproduction, the antioxidant system, and cellular energy content; however, the effects were most pronounced in the TPhP-exposed group. Transcriptomic analysis revealed that genes involved in genetic processes, immune system, and nervous system were significantly modulated by TPhP exposure. These findings suggest that some OPFRs may be as toxic as BFRs and should be used with caution.