Self-Organizing Map (SOM) is an unsupervised learning neural network and it is used for preserving the structural relationships in the data without prior knowledge. SOM has been applied in the study of complex problems such as vector quantization, combinatorial optimization, and pattern recognition. This paper proposes a new usage of SOM as a tool for schema transformation hoping to achieve more efficient genetic process. Every offspring is transformed into an isomorphic neural network with more desirable shape for genetic search. This helps genes with strong epistasis to stay close together in the chromosome. Experimental results showed considerable improvement over previous results.