Irrational spatial organization is a major problem and challenge for spatial planners. To solve this problem, spatial planners use different sets of methods and techniques, including spatial optimization. The subject of this paper is to apply methods and techniques of spatial optimization in the reorganization of the functional-spatial structure of the City of Rijeka. The aim is to present spatial optimization as a set of techniques and methods that seek to achieve rational allocation of functional zones, thereby achieving greater accessibility of urban functions, that is, a better functional-spatial structure, all with minimal financial costs and in the most environmentally friendly manner. In order to achieve this, an allocation model (simulating the state of the functional-spatial structure of the City of Rijeka in 2050 after spatial optimization), and a model of change ( predicts the state of the functional-spatial structure City of Rijeka in 2050 in case there is no spatial optimization) were formed. The comparison of the results is in the form of two different scenarios, with the scenario containing spatial optimization indicating better compactness and diversity of functional zones, that is, functional-spatial structure than the scenario containing no spatial optimization. The methods used in the work are multi-agent systems, genetic algorithms, ant colony optimization, GIS analysis, fieldwork, descriptive method, analogy method, mathematical modelling, scenario method, cellular automata, artificial neural networks, real estate costing method, statistical and geostatistical analysis and methods of landscape metric.