To investigate the role of the prkd1 gene, a typical member of the protein kinase D (PRKD) family, in early heart development, zebrafish was used as an animal model in this study. Through prkd1 knockdown with morpholino antisense oligo (MO), it was found that knockdown of prkd1 resulted in abnormal cardiac de-velopment, such as pericardial edema, cyclization disorder, cardiac tube linearization. Zebrafish heart rate analysis indicated that, compared with the wild type, prkd1 knockdown zebrafish exhibited early arrhythmia. High-throughput transcriptome sequencing was performed for zebrafish embryos at 3 days post fertilization (dpf) in control and prkd1 knockdown groups. Differential gene enrichment analysis revealed that prkd1 knockdown was significantly associated with heart-related signaling pathways, such as the adrenergic signaling pathway in cardiomyocytes. Additionally, the results of high-throughput sequencing were confirmed by qRT-PCR, which showed that some genes associated with the cardiovascular system were markedly down-regulated. Meanwhile, identification of the essential factors in early heart development revealed that key cardiac regu-latory genes like tbx5a and gata4 were significantly down-regulated. These findings suggest that the prkd1 gene may affect early cardiac development by regulating cardiac development-related signal pathways and key genes, and play an important role at the early stage of heart development.