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The microbial world represents the most important and diverse group of organisms living on earth. Because of this huge microbial bio complexity, high-throughput molecular tools allowing simultaneous analysis of existing populations are well adapted. Oligonucleotide micro array technologies have been widely used for gene detection and gene expression quantification, and more recently, they have been adapted to profiling environmental communities in a flexible and easy-to-use manner. Designing DNA micro arrays requires special attention to the design of specific and efficient probes in order to obtain an image of the microbial communities close to reality. The rapid growth of datasets, particularly environmental datasets, has led to an important increase in computational capacity requirements coupled with a fundamental change in the way algorithms are designed. Consequently, High Performance, including cluster and grid computing represents a solution to reduce the execution time of probe design algorithms in complex environments. In this paper, we present a method to parallelize probe design program for phylogenetic micro arrays dedicated to microbial ecology on distributed architecture. We implemented a mechanism that generates and monitors jobs over a grid. We obtained a complete design for 3513 genera including fungi and prokaryotes.