Genetic diversity of 12 families of the giant tiger shrimp (Penaeus monodon) that will be used in the genetically improved program was examined (N = 16/family) using microsatellites, CUPmo13 and DTLPm109. A total of 12 alleles and 32 genotypes were found at the CUPmo13 locus. Two to eight alleles were found in each family. The average heterozygosity across overall specimens was 0.82. Likewise, high genetic diversity was found at the DTLPm109 locus. Twenty-six alleles and thirty-seven genotypes were found at this locus. Three to ten alleles were found in each family.The average heterozygosity across overall specimens was 0.91.The excess number of alleles per locus in several shrimp families suggested that each apparent family may actually mixed by shrimp from different families caused by the combination of larvae from different families during the larval production. Alternatively, a female broodstock may have artificially inseminated by spermatophores from more than one male. Data about genetic diversity and genotypes of these shrimp families are useful to assist the family selection scheme for genetic improvement of P. monodon for sustainability of the shrimp industry.