We analysed the effect of temperature, coupled with food ingestion rate (IR), on the fatty acid (FA) profile of female and male clams conditioned in two groups: L (low IR at 14 and 18°C) and H (high IR at 18 and 22°C). Significant differences for group L, both 18L and 14L with low IR and slow gonadal development, owed to differences in energy balance between 18L clams (negative energy balance) and 14L clams (positive energy balance). Plasmalogens (DMA 18:0) and non-methylene-interrupted FAs might protect against reactive oxygen species and preserve the integrity of the cell membranes during food stress in 18L clams. Differences in composition for group H, both 18H and 22H with high food intake, positive energetic balance and complete and similar gonadal occupation index (GOI), probably owed to the greater energy levels at 18°C than at 22°C. Clams at 22°C H increased the oxidation of short-chained PUFA 18:3x3 and 18:3x6 to maintain the same GOI as 18H clams. Regarding the sexual differences, the greater accumulation of 20:5x3 and 20:4x6 in females might be related with oocyte maturation and release during spawning, while the greatest levels of 22:6x3 in males might be involved in spermatocyte membranes synthesis.