Amplified consensus genetic marker (ACGM) is a PCR-based marker technique that uses primers designed within conserved regions of coding sequences. After a comparison of Cryptomeria japonica and Arabidopsis ESTs to search for conserved sequences, 237 single e-PCR products were obtained. We randomly selected 110 candidate ACGM markers to test. Of the 110 candidate ACGM markers tested, 106 yielded stable and clear PCR products in C. japonica. We then tested the utility of these 106 primer pairs in 10 species, representing 7 genera of Taxodiaceae. The number of specific amplification primer pairs among those 10 species varied from 49 to 103 (or 46.2~97.2%). The 106 primer pairs (ACGM loci) were high transferable to Cryptomeria fortunei Hooibrenk (97.2%) but were low in Metasequoia glyptostroboides (46.2%). The number of PCR bands per primer pair ranged from 1.06 to 1.15, which means that most of the ACGM primers can obtain a single band within these 10 Taxodiaceae species. In summary, our study shows that ACGM is a technique applicable for marker development even in species with limited sequence data. Amplified consensus genetic marker (ACGM) is a PCR-based marker technique that uses primers designed conserved regions of coding sequences. After a comparison of Cryptomeria japonica and Arabidopsis ESTs to search for conserved sequences, 237 single e-PCR products were obtained. We randomly selected 110 candidate ACGM markers to test. Of the 110 candidate ACGM markers tested, 106 yielded stable and clear PCR products in C. japonica. We then tested the utility of these 106 primer pairs in 10 species, representing 7 genera of Taxodiaceae. number of specific amplification primer pairs among those 10 species varied from 49 to 103 (or 46.2 to 97.2%). The 106 primer pairs (ACGM loci) were highly transferable to Cryptomeria fortunei Hooibrenk (97.2%) but were low in Metasequoia glyptostroboides %). The number of PCR bands per primer pair ranged from 1.06 to 1.15, which means that most of the ACGM primers can obtain a single band within these 10 Taxodiaceae species. In summary, our study shows that ACGM is a technique applicable for marker development even in species with limited sequence data.