How to work one by hand
Put one parent's gametes along the top and the other's down the side. Fill each box with the allele from its row plus the allele from its column, writing the dominant one first so Aa never reads as aA. Then count.
The genotype ratio is the tally of the actual combinations. The phenotype ratio groups together everything that looks the same, so under complete dominance AA and Aa collapse into one group. Aa x Aa is 1:2:1 by genotype and 3:1 by phenotype, and questions frequently ask for one while students answer with the other.
Common questions
How do I actually do a Punnett square?
Write one parent's gametes across the top and the other's down the side, then fill each box with the alleles from its row and column. For a single gene each parent gives two gametes, so you get a 2x2 grid. Count the boxes to get genotype ratios, then group them by appearance to get phenotype ratios.
What is the difference between genotype and phenotype ratio?
Genotype ratio counts the actual allele combinations, like 1 AA : 2 Aa : 1 aa. Phenotype ratio counts what you would see, and since AA and Aa look identical under complete dominance, that same cross is 3 dominant : 1 recessive. Exam questions often ask for one and get answered with the other.
Why does Aa x Aa give 3:1?
Four boxes: AA, Aa, aA and aa. Three of the four carry at least one dominant allele, so three quarters show the dominant trait. The 1 in 4 chance of aa is where the recessive phenotype comes from, and it is why recessive conditions can skip generations.
What is a test cross for?
To find out whether an individual showing the dominant trait is AA or Aa, which you cannot tell by looking. Cross it with aa. If any offspring are recessive, the unknown parent must have been Aa.
How many boxes should a dihybrid square have?
Sixteen, because each parent heterozygous at two genes makes four gamete types. In general a parent heterozygous at n genes makes 2 to the power n gametes, so the square is that number squared.
Related tools
Punnett square calculator, to check any cross.
Dihybrid cross calculator, for the 16-box version.
Blood type Punnett square, for ABO and Rh.