Endophytic fungi are microbes that live asymptomatically inside plant tissues. Accumulating research studies suggest that endophytic fungi have a fundamental influence on the fitness and competitiveness of their host plants. Here, we surveyed the species diversity and community structure of endophytic fungi associated with the seeds of common ragweed (Ambrosia artemisiifolia L.), which is a notorious invasive weed belonging to the Asteraceae family in China. The main objective was to document the distribution of the fungal symbionts and to determine at what point endophytic fungi affect seed germination and seedling development in common ragweed. Endophytic fungi were found in all common ragweed populations collected from six study locations in China, with fungal isolation rates ranging from 19% to 92.63%. Yet, the isolation rates of endophytic fungi were significantly different (P < 0.01) among all six locations, with the highest isolation rate being obtained from seeds collected from Langfang City, Hebei Province. The endophytes in common ragweed seeds were predominantly isolated from involucre, with the isolation rate reaching 65.52%. The fungal isolation rates were 21.74% for seeds and 18.18% for bracks, respectively. Five fungal genera were detected in common ragweed seeds collected from Changle City, Fujian Province. The most frequent genera of the endophytic community were Alternaria and Fusarium, which accounted for 82.26% and 9.68% of isolates, respectively. Three genera were indicated as rare endophytes in common ragweed seeds, none of which exceeded 5% of isolates. Our data indicate that endophytes from common ragweed seeds are horizontally transmitted to the next generation, because no endophytic fungi were detected in newly developed seedlings. After determining the fungal genera and their relative abundance, an experiment was conducted with fermentation broths from seven representative isolates of common endophytic fungi that are present in A. artemisiifolia seeds. The germination of common ragweed seeds and subsequent seedling development were inhibited when seeds were treated with fermentation broths from seven endophytic fungal isolates. The germination of common ragweed seeds noticeably declined (P < 0.01) when treated with fermentation broths of the seven selected fungal isolates. Fermentation broths of strain AM-17 and AM-8 had the highest inhibition effects on seed germination. The germination percentages of seeds treated with strain AM-17 and AM-8 fermentation broths were 14.92% and 17.11%, respectively, whereas the germination percentage of seeds treated with water (control) reached 86.52%. The experiments also showed that the growth of common ragweed seedlings is inhibited by treatment with fungal fermentation broths. Four out of seven fungal fermentation broths significantly (P < 0.01) reduced the aboveground stem length of common ragweed seedlings when compared to the water treatment (control). Strains AM-8 and AM-17 inhibited seedling growth the greatest. Six of seven fungal fermentation broths significantly (P < 0.01) reduced the root length of seedlings, while all fungal fermentation broths significantly (P < 0.01) reduced lateral root number. In striking contrast, lateral roots failed to develop when seedlings were treated with the fermentation broth of strains AM-17 and AM-8. Five out of the fermentation broths significantly (P < 0.01) reduced the biomass of common ragweed seedlings. Seventy-seven percent of seedlings were dead after treatment with the fermentation broth of strain AM-17 for 5 days. Seed survival was not severely (P > 0.05) affected by fungal fermentation broth treatments. Seed viability analysis indicated that most seeds (50%-87.5%) were viable after the various fungal fermentation broth treatments. Our data demonstrate that metabolites produced in fungal fermentation broths do not facilitate seed germination, but did not kill the seeds.