Native potatoes are an important source of biotic/abiotic resistance and quality traits improvement. The aim of this study was to analyse genetic diversity and population structure using 14 simple sequence repeat (SSR) markers and 51 distinctness, uniformity and novelty (DUS) phenotypic traits in native potato collection (94 accessions) in India representing sub-tropical plains (45), north-west (NW) hills (25), north-east (NE) hills (22) and two unknown sources. Polymorphic 14 SSR loci revealed 97 alleles, where allele sizes per marker ranged between 75 bp (STM0037) and 296 bp (STM5114), and the number of alleles per marker varied between 2 (STI0030) and 13 (STPoAc58/STM0031). The polymorphic information content (PIC) of SSR was found between 0.29 (STI0030) and 0.90 (STPoAc58/STM0031). The accessions were grouped into four major clusters using both SSR and phenotypic traits separately based on the Jaccard similarity coefficient using the neighbour-joining clustering approach by the DARWin software. However, both clusters contained different accessions and intermixing was observed amongst collection sources. Clusters were supported by principal component analysis (PCA) plots based on both SSR and phenotypic data. Population structure analysis revealed four populations using the SRUCTURE software based on the SSR data. Taken together, our study suggests that SSR and DUS trait profiling are the key components of genetic diversity and population structure analysis in the potato. This would be useful for genetic fidelity testing of true-to-type accessions in future.