Fish identification is one of the important aspects of fisheries management. This process is occasionally challenging for small/juvenile bigeye tuna (Thunnus obesus) and yellowfin tuna (Thunnus albacares) due to their similar characteristics in size and external appearance. Morphometric and meristic techniques are difficult to apply if the fish has been damaged caused by the interaction with the fishing gear. The genetic approach requires a specific laboratory and analysis process which is very time-consuming and expensive. One method to identify fish quickly and cheaply is by otolith shape analysis. This study uses otolith shape analysis to identify small bigeye and yellowfin tuna. A total of 115 bigeye tuna otoliths and 186 yellowfin tuna otoliths were collected from several fishing ports in Indonesia, i.e.: Padang, Palabuhanratu, Bitung, and Sorong. The shape of the otolith was obtained using a qualitative analysis which was transformed by wavelet. Statistical analysis of the otolith shape using multivariate analysis in eight classifications based on locations and length class. There is a significant difference between the shape of otolith bigeye tuna and yellowfin tuna in all eight classifications (p<0.05). The difference in the otolith shape of this otolith is detected in the rostrum and antirostrum. This difference is present in all locations, particular locations, and in several length classes. The results of this study indicate that otolith shape analysis had the potential to use as a method to identify small bigeye tuna and yellowfin tuna.