The Munc13/UNC-13 family protein Ync13 is essential for septum integrity and cytokinesis in fission yeast. To further explore the mechanism of Ync13 functions, spontaneous suppressors of ync13 mutants, which can suppress the colony-formation defects and lysis phenotype of ync13 mutant cells, are isolated and characterized. One of the suppressor mutants, bst1-s27, shows defects in the cytokinetic contractile ring constriction, septation, and daughter-cell separation, similar to bst1Δ mutant. Bst1, a predicted GPI inositol deacylase, was an uncharacterized protein in fission yeast. It localizes to the nuclear ER and puncta structures in the cytoplasm. The Bst1 puncta overlaps frequently with Anp1, which is a marker of ER-Golgi transport, but rarely with trans-Golgi marker Sec72. The nuclear ER signal of Anp1 increases in bst1Δ mutant, whereas Sec72 localization shows no obvious changes. In addition, more cytoplasmic puncta structures of COPII subunits, Sec13 and Sec24, are observed in bst1Δ mutant, and acid phosphatase secretion is compromised without Bst1. Consistently, the division site targeting of the β-glucanase Eng1 and α-glucanase Agn1 is reduced in bst1Δ and bst1Δ ync13Δ mutant. Taken together, our results suggest that Bst1 regulates ER-Golgi transport and is involved in cytokinesis through regulating the secretion of glucanases.