Over 450 potato varieties and landraces are preserved as in vitro cultures by the Plant Biotechnology department of Estonian Crop Research Institute. This collection contains germplasm from various countries as well as old Estonian landraces. These potato accessions are periodically grown in the field for verification; however, this is not always sufficient to validate varieties and, in many cases, the true origin or identity of old landraces is not known. A reliable and cost-effective method for fingerprinting Estonian potato germplasm needed to be implemented. Simple sequence repeat (SSR) markers are known as robust and efficient markers for the identification of tetraploid potato. Here, fingerprinting results are presented for 103 genotypes from the Estonian potato collection using 8 SSR markers. It was shown that as few as three markers were sufficient to yield unique fingerprints for the given set of samples. SSR markers were used to estimate the allele copy number with varying success. Additionally, the reproducibility of four of these markers was assessed in two different laboratories, and repeatable results were observed. It was verified that the putative landrace ‘Kuldkera’ has the same genetic fingerprint as the variety ‘Ando’, whilst an expected clone of ‘Early Rose’ is a completely different genotype. Implementation of genetic fingerprinting and these results is of high importance for further potato genebank management and Estonian breeding programme.