Fatty acids (FAs) from blubber are often analysed to assess the diet of marine mammals. However, distribution of blubber FAs is not necessarily uniform along the body. It is therefore important to understand the deposition of dietary fat to be able to estimate the diet. We analysed the FA compositions of the thoracic ventral (T region) blubber of 28 New Zealand (NZ) sea lions Phocarctos hookeri by-caught by the southern arrow squid Nototodarus sloani fishery. Each blubber sample was divided into an inner and an outer layer. For 16 of these 28 animals, the pelvic dorsal (P) region was also sampled. The influence of body region and layer was statistically tested on the distribution of blubber FAs. We found minimal differences between the P and T regions (3 out of 29 FAs). The outer blubber layer was more concentrated in short-chain monounsaturated FAs, and less concentrated in saturated FAs, but the degree of stratification was small. Diet predictions from quantitative FA signature analysis (QFASA) applied on different body regions were similar. When applied to different blubber layers, QFASA gave some variation in the contribution of rattails (~25 % in outer blubber vs. ~12 % in inner blubber). Nonetheless, diet predicted from both layers was dominated by similar prey species: octopus, hoki and rattails. Hoki and rattails shared a similar ecological niche. Therefore, feeding ecology of NZ sea lions inferred from the inner or the outer blubber would lead to the same conclusions. In the case of NZ sea lions, the outer layer of blubber, if the only sample accessible, could be a useful tissue for diet inference from FAs.