This dissertation explores the genetic basis of gene expression in Fundulus heteroclitus by focusing on the role of the environment and its effects on gene expression and by making direct estimates of heritability using cDNA microarrays. The second chapter describes the utility of F. heteroclitus cDNA microarrays for studies of F. heteroclitus which seek to understand the genetic variation in gene expression. Measurements of mRNA fluorescence and concentration as well as differences in sample preparation and sampling of blood from a single individual over time demonstrate that F. heteroclitus cDNA microarrays are quantitative, reproducible and consistent. The third chapter examines the effect of the environment and genetic factors on the variation of gene expression. F. heteroclitus cDNA microarrays are used to determine whether a genetic component of gene expression can describe the variation in gene expression between inbred and outbred individuals from the same population. The results show that variation in mRNA expression is related to the genetic variation among individuals within a group. While chapter three reveals that there is a genetic component of variation in gene expression, the percentage of genes that are significantly heritable was not known. In the fourth chapter, the heritability of the variation in gene expression is estimated to determine the genetic basis of gene expression in F1 individuals from natural, outbred populations of F. heteroclitus. The data presented in chapter 4 are the first to formally estimate the genetic component of gene expression in F. heteroclitus. The estimates of heritability range from 0.25 to 0.86 depending on the estimation method with approximately 6.5% of genes having significant heritability. The results presented in this dissertation support the concept that genetic variation affects variation in mRNA expression among natural populations of F. heteroclitus. Natural, heritable variation in gene expression is important for understanding evolutionary adaptation and the role of natural selection in evolutionary processes.