The zooplankton communities of the Kerguelen ecosystem can be divided into the inshore, Morbihan Gulf and the shelf systems. Plankton in the Gulf displayed a high biomass and a strong seasonality with winter lows and spring and summer highs. On the shelf, the seasonality is similar but with lower levels of biomass. Zooplankton diversity is very low in the Gulf and showed an increase in species number towards oceanic waters. Energy transfer through the trophic food web was considered for the inshore system and seasonality in lipid accumulation is one of the major processes regulating the lipid availability. The main copepod, Drepanopus pectinatus (Brady, 1883), transforms low energy phytoplankton into high energy prey, showed high biomass and high lipid accumulation in the form of wax esters in spring and summer associated with 18:4 and 20:5 n-3 PUFA. A similar trend is observed for the copepod Paraeuchaeta antarctica (Giesbrecht, 1902) but because it reproduces in winter, it represents an important source of 20:5 during winter lows. The hyperiid Themisto gaudichaudii Guérin-Méneville, 1825 showed maximum lipid accumulation in the form of triglycerides in winter with a balanced supply of EPA and DHA (20:5 and 22:6n-3). Predation by higher predators such as fish larvae or nesting petrels showed differential predation pressure on zooplankton: fish larvae consumed essentially late stages of D. pectinatus while petrels fed mainly on adult stages of T. gaudichaudii and to a lesser extent P. antarctica. The main energy flow towards higher predators is well balanced between the different constituents of the zooplankton food web, but in terms of trophic upgrading and supply of essential fatty acids, T. gaudichaudii and Thysanoessa macrura G.O. Sars, 1983 appears to be the best compromise with a balance supply of both triglycerides and wax esters and high percentages of both EPA and DHA needed for the growth of most marine organisms.