The possibility of increasing n-3 and n-6 long-chain polyunsaturated fatty acids (PUFA) content in microalgal mixtures used to feed Tapes philippinarum larvae was explored by lowering culture temperature from 26 to 14 °C. Although fatty acid composition of different microalgal species has a genetic basis, the algal cultures grown at 14 °C significantly increased the content of long-chain n-3 PUFA in Isocrysis galbana and in Thalassiosira pseudonana, while in Tetraselmis tetrathelo, the PUFA increase only involved shorter chain PUFA, namely 16:4n-3 and 18:4n-3. However, larvae fed on the PUFA enriched microalgal mixture did not show improvements in growth and survival performances with respect to the control group fed the microalgal mixture grown at 26 °C. From a biochemical perspective, two key aspects emerged from the results: (i) clam larvae have adequate biotransformation and selection skills to adjust fatty acid profile to their requirements as they can even modulate the incorporation of essential long-chain PUFA as 20:5n-3 and 22:6n-3 when the dietary supply exceeds the physiological requirements; (ii) bivalve can biosynthesize non-methylene-interrupted dienoic (NMID) fatty acids as confirmed by the constancy of relative proportion with larvae growth in spite of the NMID fatty acid absence in the diet.