We report the direct imaging of a novel modulated flux striped domain phase in a nearly twin-free YBCO crystal. These domains arise from instabilities in the vortex structure within a narrow region of tilted magnetic fields at small angles from the in-plane direction. By comparing the experimental and theoretically derived vortex phase diagrams we infer that the stripe domains emerge from a first-order phase transition of the vortex structure. The size of domains containing vortices of certain orientations is controlled by the balance between the vortex stray field energy and the positive energy of the domain boundaries. Our results confirm the existence of the kinked vortex chain phase in an anisotropic high temperature superconductor and reveal a sharp transition in the state of this phase resulting in regular vortex domains.