Background and Objectives Mucinous adenocarcinoma is a distinct subtype of colorectal cancer (CRC) with a worse prognosis when compared with non‐mucinous adenocarcinoma. The aim of this study was to compare somatic mutations and copy number alteration (CNA) between mucinous and non‐mucinous CRC. Methods Data from The Cancer Genome Atlas‐colon adenocarcinoma and rectum adenocarcinoma projects were utilized. Mucinous and non‐mucinous CRC were compared with regard to microsatellite status, overall mutation rate, the most frequently mutated genes, mutations in genes coding for mismatch repair (MMR) proteins and genes coding for mucin glycoproteins. CNA analysis and pathway analysis was undertaken. Results Mucinous CRC was more likely to be microsatellite instability‐high (MSI‐H) and hypermutated. When corrected for microsatellite status the single‐nucleotide variation and insertion‐deletion rate was similar between the two cohorts. Mucinous adenocarcinoma was more likely to have mutations in genes coding for MMR proteins and mucin glycoproteins. Pathway analysis revealed further differences between the two histological subtypes in the cell cycle, RTK‐RAS, transforming growth factor‐β, and TP53 pathways. Conclusions Mucinous CRC has some distinct genomic aberrations when compared with non‐mucinous adenocarcinoma, many of which are driven by the increased frequency of MSI‐H tumors. These genomic aberrations may play an important part in the difference seen in response to treatment and prognosis in mucinous adenocarcinoma.