The paper proposes a new and innovative biologically oriented idea in conceiving intelligent systems in modern factories of the future. The intelligent system is treated as an autonomous organization structure efficiently adapting itself to the dynamic changes in the production environment and the environment in a wider sense. Simulation of self-organizing assembly of mechanical parts (basic components) into the product is presented as an example of the intelligent system. The genetic programming method is used. The genetic-based assembly takes place on the basis of the genetic content in the basic components and the influence of the environment. The evolution of solutions happens in a distributed way, nondeterministically, bottom-up, and in a self-organizing manner. The paper is also a contribution to the international research and development program intelligent manufacturing systems, which is one of the biggest projects ever introduced.