Mushtaq, it depends on the bacteria type and your task. You can easy calculate most frequent repeated DNA fragments for complete genome of closest relative of your target, and use them for hybridization in RFLP analysis as probes (not primers). Do you like to use RFLP for genetic variation study in bacterial population? Maybe, it is better to use oligos homologous to transposones or tRNA genes...
For RAPD you need to test as more primers as possible using 2-3 strains and select the best ones for all the rest bacteria. You can use as well primers in pairs.
It is better to take BOXA primer and maybe REP and ERIC - they were used in many experiments. . If you digest DNA with rare cutters before RAPD, you will have more reproduciable results. Anyway, it is better to apply single adapter AFLP instead of RAPD - this method is suitable for agarose gel.
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