<p>Seed microbiomes represent the first colonization of the plant by microbes and influence community assembly of subsequent microbes. The role that parental genotype and species of origin play in structuring and sourcing the seed microbiome is crucial to understanding the seed microbiome and patterns in microbiome variation. Seed-borne microbes become part of the seedling microbiome and have the potential to influence seedling traits and whether variation in seedling traits can be explained by seed fungal and bacterial microbiome characteristics is important to improving our ability to predict seedling-microbiome trait responses <i>a priori</i> for application. Unfortunately, the relationship between seedling traits or germination response and seed microbiome characteristics have only been quantitatively linked in one study to our knowledge. So, here we grew individuals of a wild collection of the annual grass, <i>Brachypodium distachyon</i> and inbred lines of a congener, <i>Brachypodium hybridum</i>. We grew plants in a greenhouse for seed production and used high throughput amplicon sequencing to characterize offspring seed microbiome. We also characterized the growth of sibling seedlings to those sequenced. We found that for only one of the eight traits evaluated, seed germination during cold stratification, the abundance of the most prevalent microbial families had a marginal positive influence on whether germination happened during cold stratification (<i>R</i>^<i>2</i> = 0.29, <i>p</i> = 0.07). These results critically show that seed microbiomes are strongly influenced by parental genotype and species and seed microbiomes may have diminishing influences on seed and seedling traits. Thus, more work is needed to realize the goal of microbiome-trait prediction.</p>