¹H NMR spectroscopy and multivariate data analysis were applied to the metabolic profiling and discrimination of wild sea buckthorn (Hippophaë rhamnoides L.) berries from different locations in Finland (subspecies (ssp.) rhamnoides) and China (ssp. sinensis). Principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) showed discrimination of the two subspecies and different growth sites. The discrimination of ssp. rhamnoides was mainly associated with typically higher temperature, radiation and humidity and lower precipitation in the south, yielding higher levels of O-ethyl β-D-glucopyranoside and D-glucose, and lower levels of malic, quinic and ascorbic acids. Significant metabolic differences (p < 0.05) in genetically identical berries were observed between latitudes 60° and 67° north in Finland. High altitudes (> 2000 m) correlated with greater levels of malic and ascorbic acids in ssp. sinensis. The NMR metabolomics approach applied here is effective for identification of metabolites, geographical origin and subspecies of sea buckthorn berries.