Authigenic molybdenum (Moauth) in marine sediments holds great potential to archive the Mo isotopic composition of seawater and biogeochemical processes. However, the factors that control authigenic Mo isotope (δ98Moauth) distribution patterns remain poorly constrained. Here, we report Mo abundances and δ98Mo compositions for bulk‐rock (bulk) and sequentially extracted fractions—including total authigenic (auth; i.e., non‐lithogenic fraction), carbonate (carb), iron and manganese oxyhydroxides, pyrite (py), and organic fractions (OM)—of authigenic carbonates recovered from various hydrocarbon seep sites in the Gulf of Mexico and the South China Sea. Extracted pyrite fractions exhibit Mo contents varying from 0.1 to 23.4 μg/g and generally dominate the Mo budget of seep carbonate rocks. Our data indicate large ranges of δ98Mobulk and δ98Moauth values relative to NIST 3134 (0.25‰), varying from 1.02 to 1.98‰ (n = 4) and from 0.15 to 3.07‰ (n = 34), respectively. The difference in δ98Mo values between carbonate and pyrite fractions of seep carbonate rocks formed under sulfidic conditions increases with higher Moauth contents, suggesting a control of dissolved hydrogen sulfide concentrations on Mo isotope fractionation during carbonate precipitation. Compared with δ98Moauth and δ98Mopy, δ98Mocarb of seep carbonate rocks formed under sulfidic conditions shows a relatively narrow range with an average of 1.98 ± 0.31‰ (1 SD; n = 10), providing constraints on the δ98Mo composition of seawater in the course of Earth history. Overall, our findings show that the δ98Mo composition of sequentially extracted phases of carbonate‐rich sedimentary rocks can provide insights into seawater‐sediment interactions and biogeochemical pathways of Mo during early diagenesis.