Despite the importance of endophytes to plant health, their dynamics in carrot, one of the most important vegetable crop worldwide, are not fully understood. Thus, we investigated carrot endophytes dynamics in greenhouse, field and laboratory trials using a set of carrot genotypes with broad genetic backgrounds and physiological characters. Endophytes communities of seed, seedling and roots of examined carrot were studied using both traditional culture based techniques and low and high throughput sequencing technologies. Results showed that carrot are colonized by divers assort of endophytic microbial taxa. Many of them could fix nitrogen, solubilize phosphorus, produce auxin and siderophores and reduce Alternaria dauci infection, confirming that endophytes play a role in carrot health and productivity. Some of detected endophytes were vertically transmitted to progeny via seeds and could be a part of carrot core microbiome that is needed for early seedling establishment. We also detected that some of carrot endophytes could be acquired through horizontal transmission from soil and with the greater soil health in an organic relative to a conventionally managed system a higher endophytes population with greater antagonistic activity against A. dauci were detected in organic trials. Finally, different carrot genotypes showed different endophytes communities within their tissue and some genotypes were more responsive to the beneficial endophytes inoculation, which indicate that it could be possible one day to start breeding for those beneficial plant microbial relationship.