Increasing interest in organic farming and consequently in the application of natural fertilisers poses a risk of modifying qualitative and quantitative composition of microorganisms’ populations living on plants fertilised with these fertilisers. Composition of epiphytic microflora on plant material intended for ensilage affects fermentation processes and stability and hygienic quality of obtained silage. Studies carried out in the years 2009-2011 were aimed at assessing the effect of fertilisation of permanent meadow with natural fertilisers (manure and liquid manure) and mineral fertilisers (NPK) on the number of selected groups of epiphytic microorganisms living on meadow sward. Plant samples were taken three times in vegetation seasons (before the 1st, 2nd and 3rd cut). In total, 207 samples of vegetation were analysed for: total number of aerobic bacteria, bacteria of the genus Enterobacteriaceae, yeasts and mould fungi. No differences in the number of studied groups of microorganisms living on meadow plants fertilised with different fertilisers applied at different doses were found. However, the number of particular groups of microorganisms depended mainly on the time of sampling.