Seed dormancy is a temporary replacement state observed in some higher plants, which prevents germination under unfavorable conditions. In several species, dormancy process is triggered by hormonal factors, initiated by ABA and precursor enzymes. In this work, we investigated the relationship between dormancy and the expression of ARP, DMR1, and NCED genes in upright and runner peanut seeds. Eight dormancy-contrasting genotypes were previously phenotyped based on germination traits, during three storage periods. Expression of ARP, DMR1 and NCED transcripts was analyzed by qRT-PCR, from endosperm and embryo tissues. Higher expression of NCED and ARP were found in embryo tissues from runner genotypes, IAC Caiapo and LGoPE-06, confirming findings in literature as to association of these genes with seed dormancy. Higher expression of DMR1 was found only in endosperm of upright materials (L7 Bege and BR1). We suggest the NCED is a functional molecular marker to identify dormancy in seeds, contributing to selection procedures of runner genotypes in peanut breeding.