Molecular data are the basis for many biological studies in the big data era. Understanding the current state of sequencing data is beneficial for researchers to better utilize the data. Plastid DNA sequences have been extensively applied in scientific studies of plants due to their easy accessibility, uniparental inheritance, and moderate rate of mutation. In this study, current situation of sequenced plastid DNA data of the vascular plants in the world were evaluated based on the GenBank database. The results showed that the proportion of sequenced species was low, with only 33.75% vascular plants having plastid DNA data. Sequenced species were unevenly sampled among lineages. The ratios of missing data are generally correlated with species richness within the lineages. The top three orders of the highest missing data ratio were Paracryphiales, Piperales, and Dilleniales, and the top three families were Triuridaceae, Pentaphragmataceae, and Xyridaceae. In the geographic space, the missing data ratio of plastid DNA of vascular plants showed a trend of latitudinal gradient, with the degree of missing data decreasing from the equator to the poles. Regions with high missing data ratio of plastid DNA usually possess high biodiversity, including many biodiversity hotspots. In addition, endemic species were generally with the high proportion of missing data in the majority of regions. Based on the results of this study, we suggest that priority should be given to data collection for groups with high missing data ratio and regions with high biodiversity, particularly for endemic species, to improve the sampling of genetic data of these species and regions.