Secure communication is an important aspect of today’s interconnected environments and it can be achieved by the use of cryptographic algorithms and protocols. However, many existing cryptographic mechanisms are tightly integrated into communication protocols. Issues emerge when security vulnerabilities are discovered in cryptographic mechanisms because their replacement would eventually require replacing deployed protocols. The concept of cryptographic agility is the solution to these issues because it allows dynamic switching of cryptographic algorithms and keys prior to and during the communication. Most of today’s secure protocols implement cryptographic agility, but cryptographic agility mechanisms cannot be used in a standalone manner. In order to deal with the aforementioned limitations, this thesis describes a lightweight cryptographically agile agreement protocol. The design of the protocol is formally verified in an automated security verification tool. The agreement of cryptographic keys and algorithms is done in a computationally efficient way and has a low communication bandwidth requirement. Protocol integration and usage is demonstrated in an Internet of things environment with special emphasis on the agreement procedure which adapts to current device capabilities. Additionally, a prototype implementation which can communicate on different network layers is presented. The implementation is tested and evaluated in an emulated network environment. The tests demonstrate agreement efficiency on different communication layers when using different types of cryptography. The scope of this doctoral thesis covers the following scientific contributions: 1. Secure layer-agnostic agreement protocol for cryptographically agile communication that is application and operating system independent. 2. Methods for integrating the protocol with applications that use different communication models, especially P2P networks and client-server environments. 3. Evaluation of protocol communication and agreement efficiency in a simulated and real network environment.