A method has been developed for the simultaneous analysis of hydroxylated and methoxylated analogs of tetrabromodiphenyl ethers (OH-tetraBDEs and MeO-tetraBDEs) and of hydroxylated and methoxylated analogs of tetrabromobiphenyl (diOH-tetraBB and diMeO-tetraBB) using high performance liquid chromatography/atmospheric pressure chemical ionization tandem mass spectrometry (APCI-LC/MS/MS) in negative ion mode. Chromatographic separation was performed on a 150 mm ODS column with acetonitrile:water (9:1, v/v) in mobile phase. Multiple reaction monitoring (MRM) was performed using the precursor [M-H]- ion for hydroxylated analogs, and the [M-Br+O]- ion for tetraBDEs and tetraBB, and their methoxylated analogs. The method was validated using cod liver oil samples spiked with nine analytes (100 ng/g) for linearity (r2 > 0.998), recovery (75-95%), repeatability (8-36% RSD), and sensitivity (limits of quantification (LOQ), 0.1-0.25 ng/g lipid for phenolic analytes and 6-80 ng/g lipid for neutral brominated compounds). The APCI-LC/MS/MS was applied to analyze tiger shark and bull shark liver samples, where their concentrations were up to 8 ng/g (lipid weight) for OH-BDEs, whereas they were up to 540 ng/g (lipid weight) for MeO-BDEs. The results were consistent with values determined by electron ionization (EI)-GC/MS. The first detection of 2,2'-dihydroxy-3,3',5,5'-tetrabromobiphenyl (2,2'-diOH-BB80) by this method was in marine sponge from Micronesia. The advantage of the LC/MS/MS method over GC/MS is that it provides rapid and simultaneous determination of OH-BDEs, MeO-BDEs, and their related analogs with a single preparation step and without the involvement of chemical derivatives. Although the method provides the different LOQ ranges between hydroxylated and neutral brominated analogs, future work could apply the method to the full range of PBDE-like contaminants present in the environment and in biota tissues.