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Seasonal changes of food sources were investigated by analysing the fatty acid profiles of digestive gland and muscle tissues of the naturally occurring clams Glycymeris nummaria in Mali Ston Bay, Croatia. Total lipids in the digestive gland and the adductor muscle showed parallel changes, with a maximum after the main spawning event in September. In the digestive gland saturated fatty acids were highly dominant (up to 82%), indicating detritus as the main food source for this species. This type of food prevailed during the autumn/winter period, in contrast to the spring/summer period when detritus was enriched with phyto- and, to a lesser extent, zooplankton. Fatty acid composition of muscles indicated highly efficient utilization of ingested food through significant retention of polyunsaturated fatty acid from the clams’ diet during the entire period investigated.