Many chemosynthesis-based communities prospering in deep-sea environments rely on the metabolic activity of sulfide-oxidizing bacteria. This is the case for vestimentiferan siboglinid tubeworms, whose demand for nutrition is satisfied predominantly by their endosymbiotic bacteria harbored in a specialized organ called the trophosome. Such chemosymbiosis leads to a significantly lower nitrogen isotope composition of the trophosome than in other types of soft tissue. However, the specific process of nitrogen utilization by siboglinids remains unclear. As a key element in the relevant enzymes (nitrogenase and nitrate reductase), molybdenum (Mo) is indispensable in the biogeochemical cycling of nitrogen. The Mo isotope composition (δ98Mo) of siboglinids is thus a potential proxy for decoding the processes involved in nitrogen metabolism. In this study, we found δ98Mo values along the chitinous tube of the vestimentiferan siboglinid Paraescarpia echinospica from the Haima seeps of the South China Sea as negative as −4.59‰ (−1.13‰ ± 1.75‰, 1SD, n = 19)—the lowest δ98Mo value ever reported for any kind of natural material. It is suggested that this extremely negative Mo isotope composition is caused by preferential utilization of isotopically light Mo by the tubeworm's endosymbionts or epibionts during nitrate reduction. Such Mo isotope signature could provide a means for identifying siboglinid tubeworms, a group of annelids that has previously escaped unambiguous identification due to the lack of mineralized skeleton, in the rock record.