Aflatoxin contamination in human food and animal feed poses a serious threat to consumer health and limits product marketability in global markets. In this study, in addition to determining the resistance of the pistachio cultivars Shahpasand, Abbasali, Kallehghouchi, Khanjari, Akbari, and Pesteh Garmeh to contamination by Aspergillus flavus and aflatoxin, the relationship between the anthocyanin content of the kernels of these cultivars, as antioxidant compounds, and the growth of A. flavus and aflatoxin production was investigated. The experiments were conducted in three replications following a completely randomized design. Pistachio kernels of the studied cultivars were inoculated with a toxigenic isolate of Aspergillus flavus at a concentration of 2×106 spores mL−1, and the aflatoxin concentration was determined using high performance liquid chromatography (HPLC). The anthocyanin content of pistachio kernels among the cultivars ranged from 5.42 to 7.51 mg per 100 g (dry weight). The Pesteh Garmeh and Akbari cultivars exhibited the lowest levels of Aspergillus flavus colonization and aflatoxin concentration, whereas the Shahpasand cultivar showed the highest levels; therefore, they were identified as the resistant and susceptible cultivars to A. flavus contamination, respectively. The results also indicated a significant difference among pistachio cultivars in terms of kernel anthocyanin content (at the 0.05 significance level). Accordingly, the highest anthocyanin content was observed in the Abbasali cultivar (7.51 mg per 100 g), while the lowest amount was recorded in the Kalleh Ghouchi cultivar (5.42 mg per 100 g). No significant relationship was found between the percentage of anthocyanin and the growth of Aspergillus flavus in pistachio kernels, nor between aflatoxin production and anthocyanin percentage