Aims The aim of our research was to isolate the compounds from the metabolites of Raoultella ornithinolytica with the activity against Candidaalbicans and to analyse the action of the compounds on the metabolic activity and morphology of the fungus cells. Methods and Results The effect of active protein fractions on the cell morphology, growth, and metabolic activity of C.albicans was analysed under a light microscope with Nomarski contrast and after staining with calcofluor-white. The LIVE/DEAD Yeast Viability Kit F-7030 FUN 1 was used for determination of C.albicans metabolic activity. The biomolecules obtained after isolation by ion exchange chromatography were further fractionated by Sephadex G-50 medium gel filtration. Then, after molecular sieve, the fractions were analysed by FTIR and SERS Spectroscopy. A subfraction was isolated from the antifungal protein fraction above 100kDa. The active subfraction identified as the glyco-protein complex caused a decrease in the metabolic activity and morphological changes of C.albicans cells. Conclusions The glyco-protein complex obtained from metabolites of bacteria Raoultella ornithinolytica possesses antifungal activity against C.albicans and shows minimal toxicity (1%) against fibroblasts. Significance and Impact of the Study Studies on the glyco-protein complex obtained from earthworm gut bacteria R.ornithinolytica can lead to their application in biological fungicide and pharmaceutical industry.