Stromalins are evolutionarily conserved multifunctional proteins with the best known function in sister chromatid cohesion. Human SA2 stromalin, likely involved in the establishment of cohesion, contains numerous potential nuclear localization (NLS) and nuclear export signals (NES). Previously we have found that the C-terminus of SA2 contains NLS(s) functional in human cells. However, the identity of this signal remained unclear since three NLS-like sequences are present in that region. Here we analyzed the functionality of these putative signals by expressing GFP-tagged C-terminal part of SA2 or its fragments in a human cell line and in the yeast Saccharomyces cerevisiae. We found that in human cells the nuclear import is dependent on a unique compound di- or tripartite signal containing unusually long linkers between clusters of basic amino acids. Upon expression of the same SA2 fragment in yeast this signal is also functional and can be easily studied in more detail.