Preharvest sprouting (PHS) could cause serious damage to grain yield and quality of quinoa, and the abscisic acid (ABA) is closely related to seed germination and seed dormancy. In this study two samples susceptible to PHS such as BBQ3 and WQ6 and two resources unsusceptible to PHS namely SBQ1 and WQ4 were used as experimental materials. Within 3 days of seed germination, they were applied with different concentrations of ABA and fluoridone (FL) to explore its impacts on the germination of two-color quinoa seeds, ABA content and the expression of ABA synthesis gene NCED, lysis gene 8′OH and signal transduction gene ABI3. The results showed as follows: (1) the application of different exogenous ABA concentrations had inhibitory effects on the seed germination of all quinoa materials, and the 25 μmol·L^-1 concentration had the best effect. Low exogenous FL concentration had a promotion effect on the seed germination of all quinoa materials and the 2.5 μmol·L^-1 concentration was the best. After the ABA and FL were applied, the germination rate of SBQ1 and WQ4 decreased and increased respectively less than BBQ3 and WQ6. (2) The endogenous ABA content of SBQ1 and WQ4 seeds in the control group was significantly higher than that of BBQ3 and WQ6 seeds, which was consistent with the results of PHS resistance and seed germination. The treatment of exogenous ABA could significantly increase the endogenous ABA content of quinoa seeds, and the ABA content of WQ4 seeds was significantly higher than that of WQ6 seeds, the endogenous ABA content of SBQ1 with slightly thicker pericarp was significantly lower than that of BBQ3. The endogenous ABA content in seeds of the four materials decreased after exogenous FL treatment, only SBQ1 reached a significant level, which was consistent with the results of seed germination. (3) In the control group, the expression levels of NCED, 8′OH and ABI3 genes of SBQ1 and WQ4 unsusceptible to PHS was respectively higher than those of BBQ3 and WQ6 susceptible to PHS. After exogenous ABA treatment, the expression levels of NCED and ABI3 genes of SBQ1 were significantly up-regulated at 12 h, the expression levels of the three genes of BBQ3 were significantly up-regulated at 6 h, and the expression levels of the three genes of WQ4 were also up-regulated later than that of WQ6. Under exogenous FL treatment, the expression levels of three genes of SBQ1 were all up-regulated, but the expression levels of NCED were significantly lower than that of 8′OH, the expression levels of NCED and ABI3 of BBQ3 were down-regulated, and the expression levels of 8′OH were significantly up-regulated. FL mainly inhibited the expression of NCED and 8′OH of WQ4, but had no significant regulatory effect on ABI3, while the promotion effect of FL on 8′OH gene expression was higher than that on NCED gene in WQ6. (4) The results of correlation analysis showed that seed germination rate and ABA content were significantly correlated with the expression levels of NCED and ABI3 genes in black quinoa and white quinoa. The results showed that the germination rate of quinoa unsusceptible to PHS was lower than that of materials susceptible to PHS, and the ABA content was higher than that of materials susceptible to PHS. Exogenous ABA could significantly inhibit seed germination, and the sensitivity of materials susceptible to PHS to ABA was higher than that of materials unsusceptible to PHS, and the expression of related genes in materials with high ABA sensitivity showed earlier response to ABA than other materials. FL can promote seed germination, but it may not directly regulate ABA synthesis by inhibiting NCED, ABI3 expression and promoting 8′OH expression, but by affecting other key binding sites.