| Eupatorium rhodochlamydeum A. Gray, 1880 |
| Eupatorium rhodopodum B.L. Rob., 1925 |
| Eupatorium rhomboideum Kunth, 1818 |
| Eupatorium richardsonii (B.L. Turner) B.L. Turner, 1989 |
| Eupatorium rigidum Sw., 1788 |
| Eupatorium riparium Regel, 1866 |
| Eupatorium rivale Greenm., 1904 |
| Eupatorium rivulorum B.L. Rob., 1926 |
| Eupatorium robinsonianum Greene, 1893 |
| Eupatorium rosalesia DC., 1836 |
| Eupatorium roseum Klatt, 1893 |
| Eupatorium rothrockii A. Gray, 1884 |
| Eupatorium ruae Standl., 1950 |
| Eupatorium rubricaule Kunth, 1818 |
| Eupatorium rupicola B.L. Rob. & Greenm., 1896 |
| Eupatorium rzedowskii (B.L. Turner) B.L. Turner, 1990 |
| Eupatorium sagittatum A. Gray, 1852 |
| Eupatorium sagittatum var. deltophyllum B.L. Rob., 1906 |
| Eupatorium salinum Standl. & Steyerm., 1944 |
| Eupatorium saltillense B.L. Rob., 1907 |