Seamounts are vulnerable marine ecosystems. In Chile, information on these ecosystems is quite scarce; thus, a compilation of information on their geographical distribution and biodiversity is presented herein. A total of 118 seamounts distributed in the Chilean EEZ are identified and characterized. Additionally, an in situ assessment was carried out on the Juan Fernandez seamounts 1 and 2 (JF1 and JF2), which were also oceanographically characterized. Phytoplankton, zooplankton, and marine invertebrate samples were collected and an exploratory fishing survey was executed using different gears. According to the bibliographical review, a total of 82 species have been collected on the JF1 and JF2 seamounts, highlighting fmdings of black coral species caught in lobster traps at the Juan Fernandez Archipelago. Submarine images of the marine substrate at JF1 and JF2 reveal characteristics attributable to the impact of bottom dredges, coinciding with the information obtained from the trawling fleet. The fishing activity was carried out primarily at JF2 (4,667 km of trawling). The monthly fishing effort increased considerably in 2002, 2003, and 2005, reaching values above 500 km of trawling and, thus, modifying the spatial structure of the resource aggregates on the JF2 seamount.