Today the knowledge–intensive industry development is carried out by the programs that combine a set of innovation and investment projects aimed at achieving a single goal and implemented in general constraints. The presence of a larger number of project characteristics (in particular, terms, resources, performers, etc.), which must be taken into account when forming the composition of the program, leads to the formulation of the problem of multicriteria optimization. As its solution, it is proposed to use an algorithm of bacterial optimization, supplemented by a procedure for forming initial positions using fuzzy logic methods.