Seed endophytes that inhabit the plant seed endosphere during all or part of the host plant life can play a key role in early developmental stages of the plant through diverse plant growth promoting mechanisms. The structure or functions of the endophytic bacteria can be affected by various abiotic and biotic factors. One of the biotic factors, the host plant genotypes in shaping seed microbiome have been well-established and suggest that plant-endophyte interaction is possibly dependent on plant genotypes. In nature, natural populations can represent the genotypic variation of the plant species when they were genetically differentiated. In other words, the endophytic bacterial performance would vary depending on the host plant populations or vice versa. From an evolutionary ecological perspective, characterizing plant genetic variation in response to endophytic bacteria is of interest because the variation indicates that the fitness difference among plant genotypes probably depends on the existence of endophytic bacteria. Therefore, in order to demonstrate their interaction in nature, population genomics of the plant species should be considered. Capsella bursa-pastoris is the dominant weedy species with worldwide range distribution. It has been used as model species in ecological studies due to its phenotypic viability and life history characteristics. This study aims to figure out the effects of seed endophytic bacteria on life history traits and natural selection of the C. bursa-pastoris, and their next generation seed microbiome. For that, at first, population genomics of C. bursa-pastoris was conducted using RAD-seq. A common garden experiment with the genetically differentiated populations and their endophytic bacterial treatments was performed. Lastly, seed microbiome of the next generation from the common garden experiment was analyzed using Nanopore sequencing. As the results of Chapter 1, natural populations of Korean C. bursa-pastoris has genetically differentiated, but the populations showed significant admixture genetic structure. In addition, their genetic distances between the testing populations were influenced by the spatial and environmental distances. These results suggested that C. bursa-pastoris in Korea were genetically mixed due to human activities and would be undergone by natural selection of isothermality gradients. As the results of Chapter 2, when the endophytic Bacillus aryabhattai was treated, the germination time of genetically differentiated populations was significantly delayed from autumn to spring compared to the control. In addition, the delayed germination time subsequently affected the post-germination life history traits, so their fruit production also decreased in case of the endophytic bacterial treatments. The endophytic bacterial treatments also significantly contribute to the natural selection on the branch number of inflorescences. Plants producing more and taller inflorescences can be selected. However, there was not observed the population specificity on the effects of the endophytic bacteria, even though the testing populations were genetically differentiated. From these results, the endophytic bacteria can modulate the germination time, so the altered germination time would make cascading effects on the post-germination traits, to fitness. In other words, this effect can be alternative survival strategy of the biennial plant species that show early germination in autumn and late germination in spring through changes to avoid the mortality events such as winter or herbicides. As the results of Chapter 3, the seed microbiome of the next generation after the endophytic bacterial treatments showed the population specificity on the all taxonomic levels. In general, Proteobacteria was pre-dominated across all the samples. Several phyla, family, and genera showed significantly differed among the samples depending on the populations. In addition, from the Nanopore sequencing, the inoculated bacterial isolates also discovered since its capacity of long-read sequencing. My thesis suggested a model system to figure out the effects of the endophytic bacteria on the life history, natural selection, and microbiome analysis of natural populations.