Merlin used hemlock to poison Morgana after he found out that she was the source of a sleeping enchantment that caused the citizens of Camelot to fall asleep. He took it from Gaius's chamber and mixed it with water and offered it to Morgana. She drank the water, getting poisoned by the hemlock in the process. After Morgause heard her scream and cry telepathically (either through magic, or through their connection as sisters, the latter more likely), she rushed to Morgana and then vanished with a teleportation spell, taking Morgana with her. Morgana survived this, and began to hate Merlin (The Fires of Idirsholas).
Morgana later used a poison similar to hemlock to poison a guard that knew her true nature (The Tears of Uther Pendragon).