Supercritical fluid extracts of New Zealand green-lipped mussels (NZGLM) have been suggested to have therapeutic properties related to their oil components. The large number of minor FA in NZGLM extract was characterized by a GC-CIMS/MS method that excels at identification of double-bond positions in FAME. The extract contained five major lipid classes: sterol esters, TAG, FFA, sterols, and polar lipids. The total FA content of the lipid extract was 0.664 g/mL. Fifty-three unsaturated FA (UFA) were fully identified, of which 37 were PUFA, and a further 21 UFA were detected for which concentrations were too low for assignment of double-bond positions. There were 17 saturated FA, with 14:0, 16:0, and 18:0 present in the greatest concentration. The 10 n-3 PUFA detected included 20:5n-3 and 22:6n-3, the two main n-3 FA; n-3 PUFA at low concentrations were 18:3, 18:4, 20:3, 20:4, 21:5, 22:5, 24:6, and 28:8. There were 43 UFA from the n-4, n-5, n-6, n-7, n-8, n-9, n-10, n-11 families, with 16:2n-4, 16:1n-5, 18:1n-5, 18:2n-6, 20:4n-6, 16:1n-7, 20:1n-7, 16:1n-9, 18:1n-9, and 20:1n-9 being the most abundant. In general, we estimated that FAME concentrations greater than 0.05% (w/w) were sufficient to assign double-bond positions. In total, 91 FA were detected in an extract of the NZGLM, whereas previous studies of fresh flesh from the NZGLM had reported identification of 42 FA. These data demonstrate a remarkable diversity of NZGLM FA.