In vitro plant propagation is a developed biotechnology, however until now there are no effective protocols for many perennials, especially for trees. High contamination of mature explants during tissue culture initiation, low multiplication and rooting during following passages are the main challenges. Aseptic culture of explants is associated with stress due to tissue damage and exposition to aggressive disinfectants and antibiotics during initiation. These could be the reasons of virulence of endophytes in following propagation. Plant-associated microorganisms were until recently seen as a problem for micropropagation, leading to contamination of in vitro explants. However recent studies showed that colonization of endophytes often play crucial role for increasing viability of in vitro and ex vitro plants. Most endophytes affect positively plant growth, providing nutrients and exhibiting antagonism to pathogens, as well as decreasing stress effects on plants. Beneficial effects were obtained in using Beauveria bassiana (J. Akello et al., 2007), Piriformospora indica and other members of family Sebacinales (P. Sharma et al., 2014), Fusarium oxysporum (A.S.Y. Ting et al., 2008), Ophistoma- like fungi (M. Mucciarelli et al., 2003), Phialocephala fortinii (M. Vohnik et al., 2003), Trichoderma harzianum and other Trichoderma species (P. Franken et al., 2012). Of bacteria, Acetobacter diazotrophicus (C.O. Azlin et al., 2007), Achromobacter xylosoxidans (A. Benson et al., 2014), Azospirillum brasilense (E.E. Larraburu et al., 2015), Azotobacter chroococcum (E.E. Larraburu et al., 2007), Bacillus subtilis (M. Vestberg et al., 2004), B. megaterium (P. Trivedi et al., 2007), Burkholderia phytofirmans (E.A. Ait Barka et al., 2000), B. vietnamiensis (M. Govindarajan et al., 2006), Enterobacter sp. (M.S. Mirza et al., 2001), Klebsiella variicola (C.-Y. Wei et al., 2014), Microbacterium sp. (M. Quambusch et al., 2014), Pseudomonas fluorescens (J. Thomas et al., 2010) ? P. putida (R. Lifshitz et al., 1987) also can beneficially influence plants. But until now it is unclear which factor is a trigger switched endophytes from mutualism to virulence. The only way to control such a change is to develop optimal conditions (time of obtaining explants, culture media composition and pH, temperature, etc.) in view to save in vitro mutualism with benefit for both host plant and the endophyte. Studies of many perennials showed the in vitro biotization to be helpful in microclonal propagation and plant rooting. Particularly, arbuscular micorhyza, ectomicorhyzal fungi, ericoid micorhyzal fungi, and wide range of bacteria influence positively plant micropropagation. Bacterial and fungal endophytes could stimulate plant growth due to activation of plant protection mechanisms, induction of systemic resistance to pathogens, phytohormone synthesis and better transport of water and nutrients. In this, the difficulties of classification and obtaining pure cultures of microorganisms are the main problems faced with.