A pod is a case that holds a plant's seeds. When you buy fresh peas from the farmer's market, they come still in their pod.
In many plants, seeds grow in groups, nestled within a pod. Peas are one such plant, and many other legumes and flowers have seed pods as well. The expression "two peas in a pod" refers to the way seeds are clustered together within the pod, and means "very similar to each other." Pod comes from the fifteenth century term podware, "seed of legumes or grain."