We used a multiple screening process to identify genes involved in salt tolerance–specific biosynthesis and metabolism in rice (Oryza sativa L.). We selected 8,275 salt tolerance–related candidate genes using expression profiles generated across four stages on a microarray containing 135,000 probes (135 K microarray) in Oryza sativa. Using our method, we screened 342 ortholog genes, and 74 pathway genes associated with salt –response–related biosynthesis. Finally, we identified six genes by comparison of pathway-network genes and orthologous genes. The six genes were anchored to the chromosomes of rice to characterize their genetic-map positions and were used to construct the phylogenetic tree. The results were verified by reverse transcription–polymerase chain reaction.