The molecular biomarker compositions of the ornithogenic sediments (YN), from Svalbard, Arctic were investigated. The results showed that n-alkanes had a bimodal pattern and their odd-even preference was not obvious. The alkanes contained unresolved complex mixtures (UCM) and relatively high levels of pristine and retene, indicating pollution from the nearby coal mines. The n-alkanols in the sediments had even-to-odd preference, and they might originate mainly from modern biota. Sistosterol, the main sterol in herbivores feces, was the dominant sterol, indicating that sitosterol might be a good biomarker of input from the birds feces in the sediments. The fatty acids of the sediments showed acid. The α-hydroxyl acids and ω-hydroxyl fatty acids were also detected in the sediments. In summary, the organic matters in the YN sediments were from the adjacent coal mines, bird feces, and plants.