Aims Seed endophytic bacterial (SEB) communities have been little studied to date, although these microorganisms may assist seeds and seedlings to cope with environmental stresses. Hyperaccumulators have become models for studying plant adaptation to extreme environments, such as metalliferous soils. This work aims to characterize the endophytic bacterial communities associated with hyperaccumulating seeds collected from their native ecosystems (nonmetalliferous or calamine soils). Methods Using 16S rRNA metabarcoding, endophytic bacterial communities were characterized for seeds from 14 Noccaea caerulescens populations. Plant genomes and environmental properties of the sites had previously been described. Results In all plant populations the metabarcoding revealed a large SEB core microbiome composed of the main phyla and sub-phyla: gamma-Proteobacteria (56.56%) > alpha-Proteobacteria (32.23%) > Actinobacteria (7.93%) > Firmicutes (3.78%). According to the literature, some operational taxonomic units (OTUs) found in the core microbiome may be related to "plant growth promoting endophytes" (PGPE). The changes in the relative abundance of phyla/subphyla were correlated to altitude, pH, and soil exchangeable elements (Al, Mg, Cd, Mn, Zn), yet the main parameters observed to drive SEB diversity were the plants' genetics. Conclusion The distinction between populations based on calamine soils and nonmetalliferous soils failed to explain the SEB communities' structural dissimilarities. In fact, the factor that best explained these dissimilarities was the plant's genetic subunit. Future research, based on transcriptomic approaches, should study the ecological roles of the SEB communities and their involvement in the adaptation of hyperaccumulators to metalliferous soils.