Femtosecond adaptive pulse shaping of 800-nm laser pulses is applied to control the multiphoton molecular excitation of the charge-transfer coordination complex [Ru(dpb)3](PF6)2 (where dpb=4,4′-diphenyl-2,2′-bipyridine) dissolved in methanol. A phase-only femtosecond pulse shaper provides a mechanism for multiparameter (128) variation of the incident field, and a closed-loop evolutionary algorithm optimizes pulse shapes within the vast search space. Molecular emission at 620 nm is used as experimental feedback which is proportional to the excited-state population in the long-lived MLCT3 (metal-to-ligand charge-transfer) state. The dominant intensity dependence of the multiphoton excitation process is removed by using second-harmonic generation (SHG) in a thin optical crystal as a general “reference” signal. Successful control of the emission/SHG ratio demands that the field adapt to the electronic structure or dynamic needs of the molecule in solution. This suggests that adaptive femtosecond pulse shaping can provide a general means of finding field shapes capable of selectively exciting molecules based on their unique optical properties.