It is empirically known that there is variation in vigilance-related behavior in captive population of the Japanese crested ibis in the Sado island. Such personality-related behavioral variation could have important conservational consequences, because of a selective advantage of less alert and more alert birds under serene and wild conditions, respectively. Our previous study determined the nucleotide sequences of the dopamine receptor D4 gene (DRD4), which is one of the most promising candidate genes related to personality-related behavioral variation, in the Japanese crested ibis. In this study, we identified eight conserved sequence regions in the DRD4 among the Japanese crested ibis, the domestic chicken and the great tit, which are likely to correspond to the sequence involved in the DRD4 function and/or expression. Subsequently, we detected four and five polymorphisms in the conserved region and in their vicinity, respectively, among five founder birds for the Sado Japanese crested ibis population. The polymorphism data obtained in this study will allow evaluation of the involvement of the DRD4 in personality-related behavioral variation in the Japanese crested ibis population in the Sado island through association study.