- ? muelleri Jentink, 1879

- Epimys borneanus Miller, 1913

- Epimys crassus Lyon, 1911

- Epimys muelleri campus Robinson & Kloss, 1916

- Epimys pollens Miller, 1913

- Epimys potens Miller, 1913

- Epimys sebucus Lyon, 1911

- Epimys valens Miller, 1913

- Mus chombolis Lyon, 1909

- Mus domitor Miller, 1903

- Mus firmus Miller, 1902

- Mus integer Miller, 1901

- Mus muelleri foederis Robinson & Kloss, 1911

- Mus validus Miller, 1900

- Rattus balmasus Lyon, 1916

- Rattus culionensis Sanborn, 1952

- Rattus muelleri (Jentink, 1879)

- Rattus muelleri balabagensis Sanborn, 1952

- Rattus muelleri credulus Chasen, 1940

- Rattus muelleri otiosus Chasen, 1935