A general wavefront fitting procedure with Zernike annular polynomials for circular and annular pupils is proposed. For interferometric data of typical annular wavefronts with smaller and larger obscuration ratios, the results fitted with Zernike annular polynomials are compared with those of Zernike circle polynomials. Data are provided demonstrating that the annular wavefront expressed with Zernike annular polynomials is more accurate and meaningful for the decomposition of aberrations, the calculation of Seidel aberrations, and the removal of misalignments in interferometry. The primary limitations of current interferogram reduction software with Zernike circle polynomials in analyzing wavefronts of annular pupils are further illustrated, and some reasonable explanations are provided. It is suggested that the use of orthogonal basis functions on the pupils of the wavefronts analyzed is more appropriate. (c) 2006 Optical Society of America.