Aspidosperma quebracho-blanco (white quebracho) and Schinopsis balansae (red quebracho) are distinctive trees of the South American Park in Argentina. Quebrachos are found in forests that have been exploited very intensively. The object of this work was the identification of biotic and abiotic factors specially fungal pathogen that affect the quality of both species and its relation with germination. Seeds where evaluated through germination test and the percentage of the incidence of fungal agents in two different years of harvest was determined. In S. balansae the germination rate was 77% and of 27% in 2000 and 2001 harvests, respectively. Associations fungi-germination were found in 2001 for Alternaria spp., Curvularia spp., and Fusarium spp., showing an coefficient of correlation = -0.84; -0.85 and -0.73 (p < 0.00004), respectively. A high percentage of vane seeds (55%) was also found in 2001 harvest, due to adverse environmental factors, specifically higher precipitations during flowering. In A. quebracho-blanco seeds, the germination rate was 50% and 90% in 2000 and 2003 respectively, with a 42% of immature seeds in 2000 harvest that was associated to high precipitations and high temperatures during flowering and ripping of fruits. The incidence of pathogens was low and did not have association to germination.