The sedimentary rocks of the basin are extensively intruded by igneous plugs, dikes and sills of Eocene to Oligocene age. Two large granitic intrusives near the center of the basin form East Spanish Peak and West Spanish Peak. Dikes of felsic to intermediate composition radiate outward from East and West Spanish Peaks. Dikes of mafic and ultramafic composition trend east-northeast to west-southwest across the basin. Basaltic sills tend to intrude along the coal beds.
The site of the Raton Basin was a coastal plain at the end of Cretaceous and beginning of Tertiary time, and has a well-preserved sequence of rocks spanning the Cretaceous-Tertiary boundary. For this reason, the Raton Basin had been studied for evidence of the iridium anomaly thought to be evidence for a large meteor impact at the end of the Cretaceous that is in turn thought to have caused the Cretaceous–Tertiary extinction event. The boundary is represented in the basin by a 1-cm thick tonstein clay layer which has been found to contain anomalously high concentrations of iridium. The boundary clay layer is accessible to the public at Trinidad Lake State Park, among other places in the basin.
Much of the mining on the Colorado side of the basin supplied the steel mills at Pueblo, Colorado. Production through 1975 was 326 million short tons (295 million tonnes). There are currently no active coal mines in the basin, although the New Elk coal mine is being permitted to reopen.
The first wells seeking to produce coalbed methane were drilled in the Raton Basin in 1982. Thousands of wells have successfully extracted coalbed methane from the Vermejo Formation and Raton Formation coals. The productive coalbed methane area now covers the central part of the basin, and straddles the Colorado-New Mexico state line. The two major producing companies are Pioneer Natural Resources (on the Colorado side) and El Paso Corporation (on the New Mexico side).