The paper presents a new Artificial Neural Network (ANN) encoding method called Assembler Encoding (AE). It assumes that the ANN is encoded in the form of a program (Assembler Encoding Program, AEP) of a linear organization and of a structure similar to the structure of a simple assembler program. The task of the AEP is to create a Connectivity Matrix (CM) which can be transformed into the ANN of any architecture. To create AEPs, and in consequence ANNs, genetic algorithms (GAs) are used. In addition to the outline of AE, the paper also presents a new AEP encoding method, i.e., the method used to represent the AEP in the form of a chromosome or a set of chromosomes. The proposed method assumes the evolution of individual components of AEPs, i.e., operations and data, in separate populations. To test the method, experiments in two areas were carried out, i.e., in optimization and in a predator-prey problem. In the first case, the task of AE was to create matrices which constituted a solution to the optimization problem. In the second case, AE was responsible for constructing neural controllers used to control artificial predators whose task was to capture a fast-moving prey.