☆ Prayer Beads are a common tool used in the Buddhist practice. Mantras are typically repeated hundreds or even thousands of times. The beads are used so that one can focus on the meaning or sound of the mantra rather than counting its repetitions. Though in Saiyuki, as is typically, this is not the intended purpose.
☆ The first time prayer beads are mentioned in during the Rikudou arc. Kouryuu gave a string of prayer beads to his friend Shuuei before the boy was named a Sanzo priest. They were the beads found of him in the river that he was rescued from as an infant. He claimed they were a "collectors' item" and that Shuuei should keep them well.
☆ Later, it was those same beads that appear to be what was hold the last bit of Shuuei together after Araya's spell. Then at some point they begin to glow brightly and protected Rikudou from the Seiten Taisei's rather, allowing him to escape with minimal injuries.
☆ During the Kami-sama arc, we see the prayer beads again. This time as Kami-sama's main force of defense. He uses them as a whip, a blade, and finally, as projectiles. He appears to be manipulating them through his strong control over his spiritual power. When he first appears, he is wrapped in them.