Imaging through atmospheric turbulence by systems with annular pupils is discussed using the Zernike annular polynomials. Fourier transforms of these polynomials are derived analytically to facilitate the calculation of variance and covariance of the aberration coefficients. Zernike annular shape functions are derived and used to calculate the Strehl ratio and the residual phase structure and mutual coherence functions when a certain number of modes are corrected using, say, a deformable mirror. Special cases of long- and short-exposure images are also considered. The results for systems with a circular pupil are obtained as a special case of the annular pupil.