The role of endophytic fungi in plant growth and development is well documented. However, endophytic fungi with growth promotion capacity have never been isolated from weeds previously. In the current study, we isolated 8 fungal endophytes from the roots of Monochoria vaginalis, a serious weed of rice paddy in Korea. These isolates were screened on Waito-C, in order to identify plant growth promoting metabolites. Two fungal isolates (M5.A & M1.5) significantly promoted the plant height and shoot length of Waito-C during preliminary screening experiments. The culture filtrates (CFs) of M5.A and M1.5 also promoted the shoot length of Echinocloa crusgalli. Gibberellins (GAs) analysis of the CFs of M5.A and M1.5 showed that these endophytic fungi secrete higher quantities of GAs as compared with wild-type G. fujikuroi KCCM12329. The CF of M5.A contained bioactive GAs (GA3, 2.8 ng/ml; GA4, 2.6 ng/ml, and GA7, 6.68 ng/ml) in conjunction with physiologically inactive GA9 (1.61 ng/ml) and GA24 (0.18 ng/ml). The CF of M1.5 contained physiologically active GAs (GA3, 1.64 ng/ml; GA4, 1.37 ng/ml and GA7, 6.29 ng/ml) in conjunction with physiologically inactive GA9 (3.44 ng/ml), GA12 (0.3 ng/ml), and GA24 (0.59 ng/ml). M5.A and M1.5 were identified as new strains of Penicillium sp. and Aspergillus sp., respectively, based on their 18S rDNA sequence homology and phylogenetic analysis.