A process for producing a lysosomal enzyme having a mannose-6-phosphate-containing acidic sugar chain, wherein the process comprising: culturing in a medium yeast cells obtained by introducing a lysosomal enzyme gene into a sugar chain biosynthetic enzyme gene mutant strain of yeast, collecting a lysosomal enzyme having a phosphate-containing sugar chain from the culture, and then treating the enzyme with α-mannosidase; and pharmaceutical compositions for treatment of human lysosomal enzyme deficiencies produced by the process. The genetic engineering technique using the yeast according to the present invention allows large-amount and high-purity production of a glycoprotein having a phosphate-containing acidic sugar chain which can serve as a labeling marker for transporting into lysosomes in cells of mammals such as human. The glycoprotein having a phosphate-containing acidic sugar chain according to the invention may be utilized as a drug effective in treatment of human lysosomal enzyme deficiencies, etc.