This paper presents a seismic sequence and structural analysis of a high-resolution three-dimensional seismic reflection survey that was acquired in June 2000 in preparation for Ocean Drilling Program (ODP) Leg 204. The seismic data were correlated with coring and logging results from nine sites drilled in 2002 during Leg 204. The stratigraphic and structural evolution of this complex accretionary ridge through time, as inferred from seismic-stratigraphic units and depositional sequences imaged by the seismic data, is presented as a series of interpreted seismic cross sections and horizon time or isopach maps across southern Hydrate Ridge. Our reconstruction starts at ~1.2 Ma with a shift of the frontal thrust from seaward to landward vergent and thrusting of abyssal plain sediments over the older deformed and accreted units that form the core of Hydrate Ridge. From ~1.0 to 0.3 Ma, a series of overlapping slope basins with shifting depocenters was deposited as the main locus of uplift shifted northeastward. This enigmatic landward migration of uplift may be related to topography on the subducted plate, which is now deeply buried beneath the upper slope and shelf. The main locus of uplift shifted west to its present position at ~0.3 Ma, probably in response to a change to a seaward-vergent frontal thrust and related sediment underplating and duplexing. This structural and stratigraphic history has influenced the distribution of gas hydrate and free gas by causing variable age and permeability of sediments beneath and within the gas hydrate stability zone, preferential path ways for fluid migration, and varying amounts of decompression and gas dissolution.