An experimental study was conducted to characterize the combined effects of flame-vortex interactions and equivalence ratio fluctuations on self-excited combustion instabilities in a swirl-stabilized lean premixed gas turbine combustor. The combustor was designed so that the fuel injector location and the combustion chamber length could be independently varied. In addition, the fuel and air could be mixed upstream of the choked inlet to the combustor, thereby eliminating the possibility of equivalence ratio fluctuations. Experiments were performed over a broad range of operating conditions and at each condition both the combustor length and the fuel injection location were varied. Dynamic pressure in the combustor, acoustic pressure and velocity in the mixing section, and the overall rate of heat release were simultaneously measured at all operating conditions. Two distinct instability regimes were observed; one near 220 Hz and the other near 345 Hz. It was also found that the strength of the instability changed significantly as the fuel injection location was varied, while the phase of the acoustic pressure and velocity fluctuations in the mixing section did not change. A time series of pressure and CH* chemiluminescence signals confirmed constructive or destructive coupling of the two instability mechanisms; the flame-vortex interaction and the equivalence ratio fluctuation interact each other and determine the instability characteristics in partially premixed conditions.