Methodologies commonly used to detect linkage of marker loci to loci affecting quantitative traits are discussed. It is shown that variances for the quantitative trait differ among marker genotypes when using F2 or pooled backcross data if linkage exists. Hence, to analyze this type of data by single factor ANOVA or other statistical techniques that assume a common variance is inadequate. Restriction fragment length polymorphism (RFLP) markers are a powerful tool in plant breeding but cost is an important drawback; hence, a methodology is suggested to obtain the minimum number of plants in F2 populations to detect such linkage.