CK1 enzymes are conserved, acidophilic serine/threonine kinases with a variety of critical cellular functions; their misregulation contributes to cancer, neurodegenerative diseases, and sleep phase disorders. The C-termini of these enzymes are thought to inhibit kinase activity by acting as pseudosubstrates. We were interested in identifying substrates of the fission yeast CK1 homologues Hhp1 and Hhp2, particularly substrates involved in DNA repair. We used quantitative phosphoproteomics to identify potential substrates of Hhp1 and Hhp2 in Schizosaccharomyces pombe and to compare between the full-length and C-terminally truncated forms.