In multispectral imaging, it is necessary to select a reduced number of filters to balance the imaging efficiency and spectral reflectance recovery accuracy. Due to the combined effect of filters and light source on reflectance recovery, the optimal filters are influenced by the employed light source in the multispectral imaging system. By casting the filter selection as an optimization issue, the selection of optimal filters corresponding to the employed light source proceeds with respect to a set of target samples utilizing one kind of genetic algorithms, regardless of the detailed spectral characteristics of the light source, filters, and sensor. Under three light sources with distinct spectral power distributions, the proposed filter selection method was evaluated on a filter-wheel based multispectral device with a set of interference filters. It was verified that the filters derived by the proposed method achieve better spectral and colorimetric accuracy of reflectance recovery than the conventional one under different light sources.