Observer-based counts and photo-identification are two well-established methods with an extensive use in cetacean studies. Using these two methods, group size has been widely reported, especially for small dolphins. Both methods may come with potential errors in estimating the group size, yet there is still a lack of comparison between both methods over a broad range of group size. Particularly, biogeographical variances in group size estimates were often mixed with methodological variances, making it difficult to compare estimates from different geographic regions. Here, group size estimates of a small, shallow-water, and near-shore delphinid species, Indo-Pacific humpback dolphins (Sousa chinensis), were simultaneously sampled using observer-based counts and photo-identification at three regions in the northern South China Sea. Data showed that dolphin group size from two methods were highly variable and associated with sampling regions. Generalized linear mixed models (GLMMs) indicated that dolphin group size significantly differed among regions. Statistical examinations further demonstrated dolphin group size could be affected by a complex combination of methodological and biogeographical variances. A common hurdle to examine potential factors influencing the estimation process is the inability to know the true group size at each sample. Therefore, other methods that could generate comparable estimates to represent true group size are warranted in future studies. To conclude, our findings present a better understanding of methodological and biogeographical variances in group size estimates of humpback dolphins, and help yield more robust abundance and density estimation for these vulnerable animals.