The aim of the paper is the investigation of weed flora dynamics in winter wheat cultivated in organic system in the years 1996-2007. The study was conducted in the Experimental Station of Institute of Soil Science and Plant Cultivation - State Research Institute at Osiny (Lublin province) in the long-term trial with organic system, which had been started in 1994 year. The analysis of weed species composition and the richness were done twice in vegetation period: in spring (tillering stage of winter wheat) and in summer (dough stage). Moreover the changes of biodiversity in time were investigated using ecological indices: Shannon diversity index and Simpson dominance index. The study showed the increasing biodiversity of weed flora in winter wheat cultivated in organic system during 12 years of research reflected in increasing number of weed species and Shannon diversity index values. At the beginning of winter wheat cultivation in organic system Simpson dominance index was high, suggesting the dominance of one or more weed species in community, but in the next years of study the index values were lower. The number of weeds differed in the years as a result of different weather conditions and effectiveness of mechanical weed control measures, but it didn't show increasing tendency.