The important role of endophyte communities in plant health is becoming increasingly recognized, yet information is still lacking about their source and functional role in early stages of plant development. Thus, we sought to determine whether endophyte communities are being vertically transmitted to offspring via seed and if so, begin to elucidate their functional role. Endophyte present in surface sterilized carrot seed and seedlings of nine genotypes were isolated using a culture dependent approach. Endophytes were detected in all plant extracts and abundance increased from seed to seedling, suggesting that vertical transmission of endophytes does occur in carrots and could differentially affect processes at various stages of plant development. Taxonomic identification of individual endophytes using their 16s rRNA or ITS partially sequenced regions, indicated that Pantoea spp. and Xanthomonas spp. were the most abundant bacterial genera in seeds and seedlings respectively, while Alternaria spp. was the most dominate fungal genera observed in both plant stages. In-vitro assays indicated that several isolates can produce siderophores and IAA, fix nitrogen and solubilize phosphate. This indicates that these communities could play a beneficial role in early carrot development and possibly promote processes that the carrot is unable to fulfill on its own. Running a pathogenicity test for detected isolates and transcriptomic profiling of host in the future can further support our findings and help to understand endophytes effect on carrot growth under real world situations.