Motivated by possible applications to meromorphic dynamics, and generalising known properties of difference-closed fields, this paper studies the theory CCMA of compact complex manifolds with a generic automorphism. It is shown that while CCMA does admit geometric elimination of imaginaries, it cannot eliminate imaginaries outright: a counterexample to 3-uniqueness in CCM is exhibited. Finite-dimensional types are investigated and it is shown, following the approach of Pillay and Ziegler, that the canonical base property holds in CCMA. As a consequence the Zilber dichotomy is deduced: finitedimensional minimal types are either one-based or almost internal to the fixed field. In addition, a general criterion for stable embeddedness in T A (when it exists) is established, and used to determine the full induced structure of CCMA on projective varieties, simple nonalgebraic complex tori, and simply connected nonalgebraic strongly minimal manifolds.