The difference between dominant and recessive alleles lies in their expression in an organism's phenotype. A dominant allele masks the effect of a recessive allele when both are present in a genotype. This means that if an offspring inherits one dominant allele from one parent and a recessive allele from another, the dominant trait will be expressed. Conversely, a recessive trait will only manifest phenotypically if the organism has two copies of the recessive allele. Understanding this genetic principle is fundamental in inheritance patterns and genetic studies.