Poly-ubiquitination through Lys63, a post-translational modification system, is emerging as a mechanism implicated in a variety of non-proteolytic functions in eukaryotic cells. This modification is mainly carried out via a unique complex formed between a canonical ubiquitin-conjugating enzyme (E2), Ubc13, and an E2-variant, Uev. To date, a wealth of functional information has been obtained mostly from animals and yeast. Here, we show that the ciliate Sterkiella histriomuscorum harbors a Ubc13 gene that encodes a putative protein exhibiting 60-64% identity with Ubc13 from organisms of diverse eukaryotic phyla. A yeast double-hybrid assay and 3D-structure modelling gave evidence that ShUbc13 is able to physically interact with ShUev; the existence of such a complex in a ciliate attests for its ancient origin. Western blotting reveals that Ubc13 is present in different stages of the vegetative cycle of S. histriomuscorum. Immunolocalization of Ubc13 and K63 polyubiquitinated proteins shows three main locations, namely the nucleus, cilia and plasma membrane. Possible functions of ShUbc13 and K63 polyubiquitination in this single-celled organism are considered with reference to current knowledge. In particular their likely involvement in DNA replication and DNA damage response is especially discussed.