Seed transmission is a key stage of infectious cycle in diseases epidemiology of seed-borne pathogens and allows seed-borne pathogens to survive and ensure their dispersion. In order to study mechanisms involved in seed transmission two model pathosystems have been developed to get rid of the randomness inherent in field experiments. Two pathogens, a bacteria (Xanthomonas campestris pv. campestris, Xcc) and a fungus (Alternaria brassicicola) were selected to study their transmission to seeds of Arabidopsis thaliana. Microscopic observations allowed us to better analyze histological interactions during seed transmission process. Vascular tissues colonization of scape by Xcc was visualized by confocal laser scanning microscopy and revealed that Xcc is confined in xylem tissues. Electron microscopy identified the different pathways of A. brassicicola silique penetration and seed colonization. Concerning Xcc, one (Xcc2828, xytA) of two tested Ton-B dependant transporters is involved in siliques and seeds colonization but is not involved in xylem colonization, indicating a propable specificity of this transporter with primary wall xylans. We also showed that two sigma54 factors differentially regulated the expression of genes linked to mobility and biofilm formation in Xcc, which constitute essential processes for seed transmission. Concerning A. brassicicola, seed colonization requires a functional osmosensor, the group III histidine kinase AbNIK1. Finally, proteins, potentially acting in the cell as molecular chaperones, seems to be involved in the transmission of pathogens to A. thaliana seeds both in Xcc (with harpins proteins) and in A. brassicicola (with dehydrins).