Bond-Graphs based system representation and genetic programming based search and synthesis can be combined for automated design of mechatronic or multi domain dynamic systems. This design scheme can be turned into an intelligent automated design system by introducing a dynamic database or knowledge library of relevant information (gathered through multiple runs of the same design scheme), which tends to help the designer in initial and final stages of the design process. The strength of Bond-Graphs in handling variety and dynamic behavior of systems from multi energy domains coupled with evolutionary search approach for machine intelligence implemented through genetic programming, leads to an ideal platform for testing and enhancing the state of available knowledge and technology for evolutionary design of physical systems as complex as found in nature. This book offers an introduction to this research area with a brief discussion about certain aspects and verification of one proposed automated design methodology for evolving mechatronic systems designs using Bond-Graphs and genetic programming.