Loquat (Eriobotrya japonica Lindl.) is an economically important subtropical fruit tree, originating and commercially produced mainly in China and Japan. The aseptic seed germination of 13 loquat cultivars, including 9 white-fleshed cultivars and 4 red-fleshed ones, was studied, and the relationship between the germination rate and the content of endogenous ABA in seeds was explored. The germination rate and the seedling height at 80 days after sowing of white-fleshed cultivars were generally higher than that of red-fleshed ones. The ABA content in seeds was generally lower in white-fleshed cultivars, and the ABA content negatively correlated with the germination rate at 80 days after sowing. A moderate detrimental effect of 75% ethanol disinfection on aseptic germination of loquat seeds was observed, especially, for the cultivar Dahongpao, and the germination rate and seedling height were reduced by around half and one-third, respectively. The addition of plant preservative mixture (PPM) to the germination medium at a final concentration of 25 mg·L−1 effectively controlled contamination when the 75% ethanol disinfection procedure was omitted.