Ammonia-oxidizing archaea (AOA) are abundant and widely distributed microorganisms in aquatic and terrestrial habitats. By catalyzing the first and rate limiting step in nitrification, these chemolithoautotrophs play a significant role in the global nitrogen cycle and contribute to primary production. Here, the carbon isotopic fractionation relative to inorganic carbon source was determined for bulk biomass, biphytanes and polar lipid bound sugars of a marine AOA pure culture. Bulk biomass and biphytanes from Nitrosopumilus maritimus showed identical carbon isotope fractionation (eDIC/bulk and eDIC/byphytanes) of ca. −20‰. The glycoside head groups were mainly glucose, mannose and inositol, and exhibited different carbon isotopic composition. In general, these monosaccharides were enriched in 13C (e −6.1‰ to −13.8‰) relative to bulk biomass and biphytanes. The fact that the carbon isotope composition of the biphytanes reflected that of the bulk biomass of N. maritimus suggests that the depletion of 13C in both biomass and biphytanes resulted mainly from the carbon isotope discrimination by the bicarbonate-fixing enzyme in the autotrophic hydroxypropionate/hydroxybutyrate cycle. Our results further revealed that lipid compounds represent suitable biomarkers for determining δ13C values of archaeal ammonia oxidizers without biosynthetic correction.