In order to examine the effects of exogenous abscisic acid (ABA) on germination and seedling growth of heteromorphic Suaeda aralocaspica seeds, we either directly sowed (long-term treatment) or presoaked (short-term treatment) the two seed morphs under different concentrations (0, 0.5, 1.0, 5.0, 10.0 μmol/L) of ABA. To further understand the molecular mechanism of exogenous ABA effects on different germination characteristics of heteromorphic seeds of S. aralocaspica, we examined the expression of three genes with known functions in seed germination:ABC transporter family protein, mitogen-activated protein kinase kinase, and DNA repair and transcription factor. Gene expression was analyzed using quantitative PCR on directly sown and presoaked seeds treated with 5.0 μmol/L ABA. The results revealed two findings:(1) For directly sown seeds, different concentrations of exogenous ABA inhibited germination and seedling growth of brown seeds significantly, while these processes in black seeds were accelerated by lower concentrations of ABA, rather than by higher concentrations. In contrast, pre-soaking promoted germination and seedling growth of both types of seed, and this effect increased at higher concentrations of ABA. (2) Quantitative PCR revealed that, for directly sown brown seeds, only the expression level of the gene for DNA repair and transcription factor increased significantly at 8 h compared to that of control seeds. In black seeds, the genes for DNA repair and transcription factor and for mitogen-activated protein kinase kinase were significantly up regulated compared to those in the control. For pre-soaked seeds, treatment with ABA markedly increased the expression levels of all three genes in brown seeds rather than in black seeds. Expression patterns of the three genes were consistent with the results of seed germination. These results suggest that presoaking with ABA may trigger the internal germination mechanism of S. aralocaspica seeds and accelerate the subsequent germination process. The stronger response of black seeds to ABA treatment may be an important adaptation to the harsh and unpredictable environment of Xinjiang desert region.