Otolith shape analysis has been often widely used for stock discrimination. Controversial results are concluded on geographical stocks between the Crozet Islands and the Kerguelen Islands, East Antarctic. In this study, six otolith shape indices (form factor, roundness, circularity, rectangularity, ellipticity, and aspect ratio) and elliptical Fourier coefficients were used to analyze the otoliths shape of Patagonian toothfish Dissostichus eleginoides (TOP) from those two regions to try to supplement the information about the stocks. Prior to analysis, the allometric effect of fish growth on the otolith morphology was examined. The principal component analysis (PCA) was used for analyzing the shape indices (SIs), the Ellipse Fourier coefficients (EFCs), and the combination of SIs and EFCs, and the success rate of classification is 51.00 %, 74.00 %, and 80.00 % for those three treatments, respectively. The overall otolith shapes of D. eleginoides from the Kerguelen Islands and the Crozet Islands are similar, although fine differences occur in the outer contours of otolith. Combined with the tagging and genetic data, the present study concluded that stock connectivity occurs for TOP between the Crozet Islands and the Kerguelen Islands. Multiple approaches, including otolith chemistry, may help elucidate the proportion and mechanism of exchange between two regions.