Even though it is a rare subtype, identifying the genetic features of thymic adenocarcinoma is valuable for a multifaceted understanding of thymic epithelial tumors. We experienced a female patient with thymic adenocarcinoma associated with thymic cysts. The tumor consisted of a solid whitish lesion (lesion-1) and a large cystic lesion with small papillary nodules (lesion-2). Microscopically, lesion-1 exhibited poorly differentiated adenocarcinoma accompanying numerous inflammatory cell infiltrates, and lesion-2 (the nodules within the cystic lesion) exhibited enteric-type adenocarcinoma. Consistent with the histological difference, whole-exome sequencing revealed that these two components exhibited distinct genetic features, except for only a few shared mutations, including CDKN2A truncation. Lesion-1 exhibited microsatellite instability-high signature with high mutation burden, for which immune checkpoint inhibitors might apply; and lesion-2 exhibited whole-genome doubling with KRAS hotspot mutation. Our case presents novel genetic features of thymic adenocarcinoma and demonstrates that distinct mutational processes can be operative within a single tumor.