Three ways you can identify pairs of homologous chromosomes?

An organism inherits one chromosome of a homologous pair from the maternal parent and the other chromosome from the paternal parent. Although both chromosomes possess the same genes and loci, they may feature different alleles, or versions, of those genes. For example, a maternally inherited chromosome in a pea plant may contain an allele that codes for a green pod, while the allele for a yellow pod may be found at the same location on the paternally inherited homologous chromosome. The differences between alleles of a gene are determined by deviations in their DNA sequences.

A diploid organism possesses two copies of each type of chromosome, with the potential exception of the sex chromosomes, in each of its cells. Humans, for example, have a total of 46 chromosomes in their cells. Human females have two copies of the sex chromosome called the X chromosome, so they have 23 sets of homologous chromosomes. Human males, however, possess one X sex chromosome and one Y sex chromosome, so they have 22 sets of homologous chromosomes, plus two sex chromosomes that are not homologous.