The global phase-out has decreased the use of polybrominated diphenyl ethers (PBDEs), thereby, rapidly increasing the production and use of their important surrogates, organophosphorus flame retardants (OPFRs). Currently, OPFRs are often found at higher levels in the environments compared to PBDEs. Although the two typical OPFRs, tris (1,3-dichloroisopropyl) phosphate (TDCIPP) and triphenyl phosphate (TPhP), have been frequently detected in marine environments with significant concentrations, their toxicity to marine organisms remains unknown. We used Oryzias melastigma to investigate and compare their developmental toxicity in marine organisms through two-generational chronic exposure. The results showed that TDCIPP and TPhP exposure shortened the body length and length of the pectoral fin of O. melastigma. Both TDCIPP and TPhP deformed the pectoral fins in the 1st fry and caused spinal curvature in adult fish. Therefore, these two chemicals may pose potential risks to marine fish and marine ecosystems. Further studies suggested that although these two chemicals caused similar developmental bone toxicity, they had different modes of modulating the expression of bone developmental genes such as, bmp4, bmp2 and runx2.