Microwaves have been used as a mutant agent to select mutant strains with high-yield and high-purity pigment. Mass spectrometry and nuclear magnetic resonance spectroscopic techniques were used to elucidate the structures of the pigment. High-performance liquid chromatography was used to measure pigment purity. The analysis of the mutant strain showed that pigment yield increased by 109% and was 98% pure. Prodigiosin in ethanol solution had good stability under ambient temperature and natural indoor light. However, prodigiosin rapidly decomposed under intense sunlight. Prodigiosin is an ecological colorant to dye fabrics, including synthetic and natural fibers. Synthetic fabrics dyed with prodigiosin, such as polyamide and acrylic, have high colorfastness to washing (≥4th grade) and antimicrobial properties (>90%) against Escherichia coli and Staphylococcus aureus. Antimicrobial properties were significantly different between synthetic and natural fabrics. The mutant strain Serratia marcescens jx1-1, with high prodigiosin yield and purity, has promising prospects in food, cosmetic, and textile industries.