This study was performed to develop microsatellite DNA markers, which are useful for linkage analyses, gene mapping and blood chimera analyses in the common marmoset (Callithrix jacchus). We searched 153 of 295 bacterial artificial clone DNA sequences of the common marmoset that were archived in the NCBI database in 2004. On the basis of the search, we designed 186 PCR primer sets. When tested using 5 unrelated individuals, we successfully detected 154 markers with PCR products, of which 80 (52%) were polymorphic and 74 (48%) were monomorphic. We assigned each of the 154 markers to a human chromosome based on BLAST searches, which was achieved by searching the entire human genome sequences using an ∼3 kb section of each forward primer sequence, including ∼1.5 kb of the upstream and ∼1.5 kb of the downstream sequences. Combining our assignment data and the chromosome painting-assisted karyotype of the common marmoset [Sherlock et al., Genomics 33:214–219, 1996], we prepared a list of 154 microsatellite DNA markers that were assigned to human chromosomes, except for the Y chromosome, which is equivalent to a chromosome map. Using five microsatellite DNA markers, we have established a fragment analysis method with a sequencer, which can be routinely used for blood chimera analysis, parentage diagnosis and individual identification. Am. J. Primatol. 71:912–918, 2009. © 2009 Wiley-Liss, Inc.