When you consider more than one characteristic at a time, using a Punnett square is more complicated. This is because many more combinations of alleles are possible. For example, with two genes each having two alleles, an individual has four alleles, and these four alleles can occur in 16 different combinations. This is illustrated for pea plants in Figure below. In this cross, both parents are heterozygous for pod color (Gg) and seed color (Yy).
Punnett Square for Two Characteristics. This Punnett square represents a cross between two pea plants that are heterozygous for two characteristics. represents the dominant allele for green pod color, and represents the recessive allele for yellow pod color. represents the dominant allele for yellow seed color, and represents the recessive allele for green seed color.
CK-12 Foundation, Biology. http://creativecommons.org/licenses/by-nc-sa/3.0/