The prevalence of bisphenol A (BPA) in the environment has attracted increasing attention because of the toxicity of this manmade pollutant. However, the toxicity related to cardiac development remains largely unknown. In the present paper, we investigated the cardiac toxicity of BPA using marine medaka (Oryzias melastigma) embryos. At 2 days postfertilization (dpf), the embryos were continuously exposed to a low concentration of BPA (200 μg/L) for the whole embryonic stage. Heart rate and sinus venosus (SV)-bulbus arteriosus (BA) distance were measured under microscopy. The mRNA expression levels of genes were quantified by SYBR real-time RT-PCR, and hematoxylin and eosin (H&E) staining was used to examine the histology of fish larvae hearts. Neither the heart rate nor the SV-BA distance of the embryos was affected by BPA exposure. However, the mRNA expression levels of Na(+)-K(+)-ATPase, BMP4, COX-1, FGF8, GATA4, and NKX2.5 were all downregulated at the critical developmental stages (6 and 10 dpf). Interestingly, the mRNA expression levels of COX-2 and LERP were significantly upregulated at 10 dpf. The mRNA expressions of inflammation-related genes (TNFα, IL1β, SOD, and CCL11) were all significantly upregulated after exposure. Moreover, we found that both the body length and the body width decreased in the larvae after embryonic exposure to BPA. The distributed foci of inflammation were observed in the juveniles after 2 weeks' depuration. Exposure to BPA at embryonic stages could alter the expression of heart development-related genes and inflammation-related genes of O. melastigma. The larvae hatched from exposed embryos showed the foci of inflammation in the heart ventricles and the decrease of the body length and width.