Using the SeaMARC II seafloor mapping tool in conjunction with closely spaced seismic reflection profiles, we have mapped a segment of the Flores back arc thrust zone. Structural irregularities along the deformation front of the thrust zone result from changing stratigraphy and basement structure of the lower plate. NE trending faults cutting the outer slope of the Flores basin are easily mapped because they truncate dense drainage patterns obliquely. Mud diapirs, probably indicating elevated fluid pressures, have formed throughout the accretionary wedge but appear to be concentrated (as do back arc thrust earthquakes) at the ends of thrust faults. The overall orientation of the deformation front of the accretionary wedge is 100¿, suggesting a NNE sense of the thrust motion and supporting an origin of the thrust zone by collision of the arc with Australia rather than by magmatic forcing or gravitational sliding or spreading. Orientations of faults and folds close to the arc are not consistent with the trends of the frontal thrusts, however, and the difference may be due to either different initial orientations or to later rotations of structural features as the accretionary wedge grew.