A new method for intrinsic terminator prediction based on Rnall, an RNA local secondary structure prediction algorithm developed recently, and two U-tail score schemas are developed. By optimizing three parameters (thermodynamic energy of RNA hairpin structure, U-tail T weight, and U-tail hybridization energy), the method can recognize 92.25% of known terminators while rejecting 98.48% of predicted RNA local secondary structures in coding regions (negative control) as false intrinsic terminators in E. coli. This method was applied to scan the genome of Synechococcus sp. WH8102, and we predicted 266 intrinsic terminators, which included 232 protein-coding genes, 12 tRNA genes, and 3 rRNA genes. About 17% of these terminators are located at the end of operons. It is also identified 8 pairs of biodirectional terminators. The method for intrinsic terminator prediction has been incorporated into Rnall, which is available at http://digbio.missouri.edu/～wanx/Rnall/.