A theoretical framework is developed for the line shapes of the single molecule spectroscopy (SMS) of multichromophoric macromolecules by combining the Hamiltonian-based line shape theory with a kinetic equation formulation of single molecule photon counting processes. The theory allows a consistent treatment of two different line broadening mechanisms, one originating from the fast quantum dynamical degrees of freedom and the other originating from slow stochastic fluctuations that can be substantial within the SMS measurement time scale. A general expression is derived for the photon counting probability, which enables simulation of SMS line shape as an average over a renewal process and makes it possible to study the effects of radiation induced fluctuations. Then conditions are clarified under which the line shape reduces to a simple average over the distribution function of slow fluctuations. Model calculations for a bichromophoric system illustrate the subtle interplay between the fast and slow line broadening mechanisms. (C) 2003 American Institute of Physics.