This book provides comprehensive coverage of Markup languages and simulators for molecular communications. The authors focus primarily on characteristics and applications with these programing tools for molecular communications. Specifically, the book emphasizes simulations with NS-3 that is simulator defined for nanocommunications (including molecular communications) with IEEE standards 1906.1 and 1906.1.1, and also simulations with MolComML (Molecular Communication Markup Language), the European version of IEEE 1906 standards. The authors discuss only the most widespread and widely used languages ​​and simulators in molecular communications. The book starts by introducing basic elements of molecular communications systems, their main languages ​​and simulators, as well as briefly discussing the IEEE nanocommunications standards. The authors then present the main programming languages ​​and simulators commonly used in molecular communications. The book establishes a complete analysis regarding digital tools to learn and to study molecular communications for possible medical and biological communications systems applications. The book is intended for telecommunications and biomedical students, engineers, masters, PhDs, and researchers.