The Hidden Markov Models (HMMs) are widely used for biological sequence analysis because of their ability to incorporate biological information in their structure. An automatic means of optimising the structure of HMMs would be highly desirable. To maintain biologically interpretable blocks inside the HMM, we used a Genetic Algorithm (GA) that has HMM blocks in its coding representation. We developed special genetics operations that maintain the useful HMM blocks. To prevent over-fitting a separate data set is used for comparing the performance of the HMMs to that used for the Baum-Welch training. The performance of this algorithm is applied to finding HMM structures for the promoter and coding region of C. jejuni. The GA-HMM was capable of finding a superior HMM to a hand-coded HMM designed for the same task which has been published in the literature.