The dominant soils of eastern and western Lithuania are acid. Liming and application of organic fertilizers are therefore the most effective ways to improve properties. Accordingly, two permanent liming and organic manuring trials were initiated in 1949 on an acid soil in the Vezaiciai Branch of the Lithuanian Institute of Agriculture. This study reports the effects of long term manuring on weed flora and topsoil seed content in the sixth rotation of crops in the long-term field experiments (1996–2002). Increasing rates of manure application from 20 to 120 t ha−1 decreases soil seed contents under acidic soil conditions. On the other hand, long-term application of increasing rates of manure did not affect the total number of weeds in limed soil. Number of acidophilic weed species was much lower and plants of Rumex acetosella were not found, but density of nitrophilous weed species increased when long-term application of increasing rates of manure took place in limed soil. Acidophilic weed plants Scleranthus annuus, Spergula arvensis,and Rumex acetosella and their seeds in topsoil dominated in the acid unmanured soil.