Pre-Tertiary metamorphic tectonites in the internal San Juan Islands fold-thrust belt are bound structurally on the north by an external belt of unmetamorphosed Mesozoic and Eocene clastic rocks. In the southwest San Juan Islands, metamorphic tectonites record four and locally five generations of penetrative structures. In contrast, external belt rocks exhibit two generations of structures. Within the internal belt, first structures (D1) are rootless tight to isoclinal folds with a pervasive shallow to steeply dipping penetrative axial-planar cleavage. Locally, D1 structures are cross-cut by shallow to moderately dipping shear zones with down-to-the NE shear sense. Superposed D2 structures are NW-trending upright to SW vergent close to isoclinal folds with a penetrative axial planar cleavage. D3 structures are open to close NE-trending upright folds with a spaced crenulation cleavage and locally are represented by NE-trending conjugate kink bands. In the south, the youngest deformation, D4, consists of NW-trending upright folds with an axial-planar crenulation cleavage. D4 folds have wavelengths up to several kilometers and control the outcrop pattern of lithologic units. Farther north in the internal belt, D4 and earlier folds and foliations are overprinted by upright NNE gentle to open folds with a spaced axial-planar cleavage (D5). In the external belt, early WNW to NW trending upright open to close folds have wavelengths up to several kilometers and are overprinted by NNE upright open to close folds with similar wavelengths. Penetrative axial-planar cleavage is locally developed but is restricted to fine-grained clastic units. Relative timing and orientation indicate that D4 and D5 in the internal belt correspond to folds in the external belt and thus are post-Eocene in age. Based on a minimum mid-Cretaceous protolith age for internal belt tectonites, D1 through D3 structures formed in the latest Mesozoic or early Tertiary. Imbrication of the internal and external belts is constrained as post-Eocene.