The design of cryptographic and security protocols for new scenarios and applications can be computationally expensive. Examples of these can be sensor or mobile ad-hoc networks and electronic voting or auctions applications. In such cases, the aid of an automated tool generating protocols for a predefined problem can be of great utility. This work uses the Genetic Algorithms (GA) techniques for the automatic design of security networked protocols. When using GA for optimizing protocols the genome definition is critical. We discuss how security protocols can be represented as binary strings. Arbitrary criteria can lead to improper strings for our GA tools. We explain and justify the steps to define genome interpretation in our optimization method. Analysis of the proposal attending is also presented as part of our contribution.