In Drosophila, sperm length and the length of the females' primary sperm-storage organ have rapidly coevolved through post-copulatory sexual selection. This pattern is evident even among geographic populations of Drosophila mojavensis. To understand better these traits of potential importance for speciation, we performed quantitative genetic analysis of both seminal receptacle length and sperm length in two divergent populations. Parental strains, F1, F1 reciprocal (F1r), F2, F2r, backcross and backcross reciprocal generations were used in a line-cross (generation means) analysis. Seminal receptacle length is largely an autosomal additive trait, whereas additivity, dominance and epistasis all contributed to the means of sperm length. Either an X-chromosome or a Y-chromosome effect was necessary for models of sperm length to be significant. However, the overall contributions from the X and Y chromosomes to sperm length was small.