To achieve high expression of glycoside hydrolase family 45 endoglucanase (RsSym45EG1) from a symbiotic protist of the termite Reticulitermes speratus, synthetic sequence RsSym45eg1-co, in which the codon usage was adjusted to that of the highly-expressed tef1 gene encoding translation elongation factor 1α, was prepared and introduced into A. oryzae. The transcript level of RsSym45eg1-co was 1.8-fold higher than that of RsSym45eg1. In cells harboring RsSym45eg1, but not RsSym45eg1-co, truncated transcripts in which the coding region was prematurely terminated and followed by a poly A chain were found. The production of endoglucanase in the culture supernatant was improved by codon optimization. Truncated transcripts were also found when cellobiohydrolase and β-glucosidase from R. speratus symbionts were expressed, and the transcript level of the former was increased by codon-optimization. Our findings suggest that premature polyadenylation frequently occurs in heterologous protein expression in A. oryzae, which might result in the poor yield of expressed proteins.