Another kind of Heart Seed is the Pretty Cure Seed (プリキュアの種 Purikyua no Tane?, Seed of Pretty Cure), which is a Heart Seed inside the heart which can only be summoned by a fairy from the Tree of Hearts. The Pretty Cure Seed is the mark of a Cure, and by putting it inside the Heart or Shiny Perfume, it is possible for those with Pretty Cure Seeds to transform. The Pretty Cure Seeds do not necessarily need to have the same color as the person's Heart Flower's Heart Seed, as Kurumi Erika's Pretty Cure Seed is dark blue despite her Heart Flower bearing a light blue Heart Seed. An advanced version of the Pretty Cure Seed is the Super Pretty Cure Seed (スーパープリキュアの種 Sūpā Purikyua no Tane?), which is used to retransform Pretty Cure into Super Pretty Cure. It is also used to enter the Pretty Cure Palace.
The Heart Perfume is also capable of holding one normal Heart Seed inside. These Heart Seeds, depending on the colors, will give the users different power-ups to use. Only three colored Heart Seeds have been seen used within the series: The red Heart Seed, shown to speed up the Cure, the turquoise Heart Seed, shown to calm the mind, and the magenta Heart Seed, shown allowing one to use her maximum power. These Heart Seed can be used when transformed and untransformed. The white Heart Seed has seen being used with the Heartcatch Mirage to teleport the girls to the Tree of Hearts in the second set of eye-catches.