[Objectives]  To increase the available information on single nucleotide polymorphism (SNP) and insertion- deletion (InDel) mutation loci in Apis cerana cerana by searching for these loci in transcriptome data obtained from the A. c. cerana larval gut. [Methods]  Based on mapping information from the A. cerana reference genome, GATK software was used to identify single base mismatches and base insertion deletions between clean reads. Annovar software was then used to analyze SNP and InDel loci. In addition, genes containing SNP or InDel loci were aligned to the GO and KEGG databases to deduce their likely function and pathway annotation. [Results]  A total of 58 919 SNPs were identified, including 24 548 homozygous and 34 371 heterozygous, sites. Among these, 4 9102 had undergone conversion and 9 817 had undergone transversion. C/T and T/G were the most and least common mutations, and most (22 649) were found in the exon region. Synonymous mutations were more abundant than non-synonymous mutations. Genes containing SNP loci were annotated to 46 GO terms and 121 KEGG pathways. A total of 6 551 InDel loci were identified, including 3 270 insertion mutations and 3 281 deletion mutations. Most (2 793) InDel loci were found in the intronic region. Frameshift insertions were the most common mutation in InDel loci. InDel loci could be annotated to 27 GO terms and 28 KEGG pathways. [Conclusion]  Over 58 000 SNP and 6 500 InDel loci were identified in A. c. cerana and the most common kinds of mutations in these genes, their distribution in various functional elements of the genome, and the codon mutation types, were analyzed. Our findings indicate the likely functions of SNP and InDel loci in A. c. cerana.