The geology and structure of the Cleft Segment of the Southern Juan de Fuca Ridge (JdFR) have been examined using high-resolution mapping systems, observations by remotely operated vehicle (ROV), ROV-mounted magnetometer, and the geochemical analysis of recovered lavas. Bathymetric mapping using multibeam (EM300) coupled with in situ observations that focused on near-axis and flank regions provides a detailed picture of 0 to 400 ka upper crust created at the southern terminus of the JdFR. A total of 53 rock cores and 276 precisely located rock or glass samples were collected during three cruises that included sixteen ROV dives. Our observations of the seafloor during these dives suggest that many of the unfaulted and extensive lava flows that comprise and/or cap the prominent ridges that flank the axial valley emanate from ridge parallel faults and fissures that formed in the highly tectonized zone that forms the walls of the axial valley. The geochemically evolved and heterogeneous nature of these near-axis and flank eruptions is consistent with an origin within the cooler distal edges of a crustal magma chamber or mush zone. In contrast, the most recent axial eruptions are more primitive (higher MgO), chemically homogeneous lobate, sheet, and massive flows that generate a distinct magnetic high over the axial valley. We suggest that the syntectonic capping volcanics observed off-axis were erupted from near-axis and flank fissures and created a thickened extrusive layer as suggested by the magnetic and seismic data. This model suggests that many of the lavas that comprise the elevated ridges that bound the axial valley of the Cleft Segment were erupted during the collapse of a magmatic cycle not during the robust phase that established a new magmatic cycle.