In the present study, to examine seasonal changes in the compositions of pond sediment and the subsequent effects on the food sources of cultured sea cucumber Apostichopus japonicus using fatty acid biomarkers, seasonal variations in the fatty acid profiles of sediment samples and A. japonicus were investigated in Jinghai Bay mariculture zone from May 2012 to December 2012. In the present experiment, ratio of 16:1(n-7)/16:0 and EPA were selected as the trophic markers for diatoms, DHA and DHA/EPA for dinoflagellates or protozoa, 20:4(n-6) for brown algae and odd-chain and branched-chain fatty acids (odd & br FAs) along with 18:1(n-7) for heterotrophic bacteria. The results showed that the sediment samples were mainly composed of diatoms, brown algae, dinoflagellates or protozoa and bacteria and their compositions showed significantly seasonal variations as evidenced by the fatty acid trophic markers. The highest ratios of 16:1(n-7)/16:0 and contents of EPA (diatoms) were observed in winter, the highest concentrations of 20:4(n-6) (brown algae) were found in autumn, the highest levels of bacterial markers (odd & br FAs) and 18:1(n-7) were detected in summer and the highest proportions of DHA (dinoflagellates or protozoa) were observed in winter. Correlation analysis showed that the food sources of A. japonicus were significantly and positively correlated with the diatoms, dinoflagellates or protozoa and bacteria. Results of present study suggested that the food sources of A. japonicus were significantly influenced by the seasonal changes in the compositions of sediment.