The present study compared the lipid composition andin vivocapability ofArtemiasp. metanauplii (the main live prey used in aquaculture) andGrapsus adscensioniszoeae (as a wild zooplankton model) to metabolise unsaturated fatty acids. The two species were incubatedin vivowith 0.3μM of individual [1- 14C]fatty acids (FA) including 18:1n‐9, 18:2n‐6, 18:3n‐3, 20:4n‐6 (ARA), 20:5n‐3 (EPA) and 22:6n‐3 (DHA) bound to bovine serum albumin (BSA). Compared to metanauplii, zoeae contained twice the content of polar lipids (PL) and eight-fold the content of long-chain polyunsaturated fatty acids (LC-PUFA).Artemiasp. metanauplii showed increased short chain fatty acidde novosynthesis from beta-oxidation of [1-14C]LC-PUFA, preferentially DHA. Of the LC-PUFA, DHA showed the highest esterification rate intoArtemiasp. triacylglycerols. In contrast, inGrapsuszoeae [1-14C]DHA displayed the highest transformation rate into longer chain-length FAs and was preferentially esterified into PL. EPA and ARA, tended to be more easily incorporated and/or retained than DHA inArtemiasp. Moreover, both EPA and ARA were preferentially esterified intoArtemiaPL, which theoretically would favour their bioavailability to the larvae. In addition to the inherent better nutritional value ofGrapsuszoeae due to their intrinsic lipid composition, the changes taking place after the lipid incorporation, point at two distinct models of lipid metabolism that indicate zoeae as a more suitable prey thanArtemiasp. for the feeding of marine animals.