An important direction of forming an effective system for recycling waste of various genesis is to optimize the processes of their treatment using the latest information resources. The paper deals with theoretical studies of directions for the systematization and optimization of anaerobic waste processing technologies using ontological tools based on information resources. Significant scientific support to biochemical research is provided by electronic bioinformatics databases such as KEGG, BacDive, and EAWAG-BBD, etc., which provide access to a collection of graphical representations and text descriptions of metabolic or signal pathways, schemes of regulation of biological processes, information about the organism. They cover various aspects of bacterial and archaic biodiversity, information on microbial biocatalytic reactions and biodegradation pathways of mainly xenobiotic chemical compounds. Also, in the course of work based on analytical data of electronic databases of bioinformatics, in particular, the interaction of necessary ecological and trophic groups of microorganisms, biochemical simulation of anaerobic waste processing with biofuel production was carried out. Keywords: waste disposal, bioinformatics database, anaerobic fermentation, biofuel.