Halogenated organic pollutants (HOPs)—including organochlorine pesticides (OCPs), polychlorinated biphenyls (PCBs), polybrominated diphenylethers (PBDEs), polybromobiphenyls (PBBs), dechlorane plus (DP), tetrabromobisphenol A (TBBPA), and hexabromocyclododecanes (HBCDs) as well as PCB metabolites (methylsulfone [MeSO2-]) and hydroxylated (OH-) PCBs and OH-PBDEs—were determined in the serum of mud carp and northern snakehead from an electronic-waste (e-waste) site in South China. The average concentrations (mean ± SD) of ΣPCBs, ΣPBDEs, ΣOCPs, ΣPBBs, ΣTBBPA, ΣHBCDs, and ΣDP were 1410 ± 324, 70 ± 20, 3.0 ± 0.4, 2.8 ± 0.8, 1.6 ± 0.4, 1.0 ± 0.2, and 0.3 ± 0.03 ng/g wet weight (ww) in mud carp and 6430 ± 781, 468 ± 49, 22.4 ± 1.1, 7.0 ± 0.6, 2.9 ± 2.3, 5.5 ± 1.1, and 4.6 ± 0.6 ng/g ww in northern snakehead, respectively. MeSO2-PCBs, OH-PCBs, and OH-PBDEs were detected at a total concentration of 0.44 ± 0.03 and 9.7 ± 0.3 ng/g ww in mud carp and northern snakehead, respectively. The congener profiles of PCBs, PBDEs, OH/MeSO2-PCBs, and OH-PBDEs were found to be significantly different between the two fish species, possibly as a result of species-specific bioaccumulation and/or metabolism of the HOPs. Chirality of ten PCB congeners and α-HBCD, as well as the fanti values of DP in the serum samples, supported the species-specific biotransformation of HOPs. Furthermore, the presence of covaried and counter-varied enantiomeric fractions of PCBs between the two fish species indicated species- and congener-specific enantiomer enrichment of PCBs.