Background: Banana shrimp Fenneropenaeus merguiensis has emerged as an important aquacultured shrimp species in South East Asia and Australia. However, the quantitative genetic basis of economically important traits in this species are currently not available, while for body colour, cooked or uncooked, there are no genetic parameter estimates for any shrimp or indeed any decapod crustacean. In this study, we report for banana shrimp genetic parameters for morphometric traits and, the first time for any shrimp, parameter estimates for body colour. Ten highly polymorphic microsatellite markers were developed from genomic sequences and used to construct a pedigree for 2000 offspring from approximately 60 female and 60 male parents that were sampled from a single routine commercial production pond. Results: Restricted maximum likelihood method applied to a single trait mixed model was used to estimate heritabilities, while correlations were estimated using the multi-trait approach. The estimates of heritability for morphometric traits were moderate to high (h2 = 0.14 – 0.50). Body colour of uncooked shrimp showed a heritable additive genetic component (h2 = 0.03 – 0.55), and those estimates obtained for cooked shrimp were significantly different from zero. Genetic correlations among morphometric traits were all positive and very high (close to unity, rg =0.85 – 0.99). The genetic correlations of body traits (weight, length and width) were positive with both colour after cooking (0.74 – 0.84) and body colour measured on live shrimp (0.59 to 0.70). The positive genetic correlations between the cooked body colour and uncooked body colour (0.64 ± 0.20) suggests these two traits can be simultaneously improved in practical selective breeding programs. This first ever report of genetic parameters for cooked or uncooked colour in crustacean indicates there is potential for genetic improvement of both growth and body colour through selection. Conclusions: In the present study we demonstrated for banana shrimp that genetic parameters can be estimated from commercial samples (using pedigrees based on DNA markers), that selection for shrimp colour should be successful under such commercial conditions.