In order to enhance heterologous cellulase protein production in yeast, a plasmid harboring the endoglucanase gene from Clostridium thermocellum (Ctcel8A) was used to systematically transform a homozygous diploid yeast deletion strain collection. We identified 55 deletion strains that exhibited enhanced endoglucanase activity compared with that of the wild-type strain. Genes disrupted in these strains were classified into the categories of transcription, translation, phospholipid synthesis, endosome/vacuole function, ER/Golgi function, nitrogen starvation response, and cytoskeleton. The vps3Δ and vps16Δ strains, which have deletion in genes encoding components of the class C core vacuole/endosome tethering (CORVET) complex, also exhibited enhanced β-glucosidase activity when Ctcel8A was heterologously expressed. Moreover, multiple gene deletion strains were constructed by using the vps3Δ strain. Endoglucanase activity of the resulting rav1Δvps3Δ double deletion strain was exhibited higher than that of the rav1Δ or vps3Δ strains. Our genome-wide analyses using the yeast deletion strain collection identified useful genes that allow efficient expression of cellulase.