In Okinawa Kenpo lineage, we practice both Sanchin and Seisan kata. Anybody who has trained in them realizes quickly that these are very different from ordinary kata. The breathing is intense, the body is tight, and the spirit is wound like a coiled snake. The positive influence on health and martial arts ability is fairly well accepted, but the origins are a cause of debate. I'd like to analyze a little bit about the backgrounds of both, starting with one important fact – they both stem from Naha-te.
It is widely believed that Naha-te was heavily influenced by Fujian White Crane style, originated in Southern China. Therefore, it could be logically asserted that white crane style has had influence upon both Seisan and Sanchin. This actually stands to reason as both kata exhibit Chinese flavors in their execution such as open hands and circular movements.
It is also pertinent to compare these kata to Hakatsuru, the white crane. This kata is known to have strong Chinese roots. I have seen two men perform Hakatsuru kata – Seikichi Odo (on tape) and George Alexander (in person). The white crane style had a softer flow than ordinary Okinawa kata. Many of the techniques were performed open hand. The breathing was reminiscent of the hard breathing as seen in Sanchin, but more shallow and not nearly as tense in the body. These styles definitely seem related, but you can tell that the Okinawans integrated their own theories (like iron body and closed fists) when making Seisan and Sanchin.
As for comparing Seisan and Sanchin against one another – it's no doubt they are sister kata. The distinctive breathing and slower, deliberate movement give it away. However, upon closer inspection, there are important differences as well. (From an Okinawa Kenpo standpoint) – The stancing is different. Seisan uses a more traditional front stance, while Sanchin uses an aptly named sanchin-dachi, utilizing heavy pidgeon toeing, short length and width, and slight kneebend. Here is a visual –
Furthermore, the deep breathing is not identical. Sanchin utilizes a '3 battles' method, in which 3 exhalations are made as the practitioners tightens the extremities, then the inner boddy, and finally the hara area. Despite having exhaled 3 times and tightened more and more on each breath, there should still be a small reserve of air in the lungs. Sanchin can be a punishing kata, but the practitioner should not be out of breath at the conclusion of the kata.
Seisan utilizes less triple exhalation and more single exhalation (That being said, I have seen some of the kata done with triple exhalation, especially at the beginning). Seisan also uses a crescent stepping method instead of sanchin-dachi movement. Crescent stepping is also known as half-moon stepping because the foot traces a half moon on the floor as it moves in toward the front foot, then out as it steps forward. This is believed to be a significant connection to the term Hangetsu, as Hangetsu can be translated as "half moon" and likely refers to the movement in the kata.
For those of you familiar with the term or kata Hangetsu –
"Hangetsu kata is the echo of the Sanchin tradition" – From what I know, Funakoshi Sensei integrated Hangetsu into Shotokan karate instead of Sanchin. Hangetsu is considered a later version of Seisan, but it integrates more Sanchin characteristics than the old style Seisan, specifically at the beginning. So Hangetsu is a version of Seisan that replaced Sanchin for Funakoshi; however, it also integrates some Sanchin theory. It's easy to see how that can get convoluted.
Whatever style you happen to train in, dig deep to see if it traces back to Naha-te. Some styles trace their lineage very clearly back to Naha-te, like Goju-ryu. Other styles have to analyze who their teachers learned from because the old okinawan masters cross-trained with each other constantly. For example, Choki Motobu was regarded as a shuri-te practitioner, and yet Sanchin was a part of his repertoire.
For some further reading regarding white crane and how it relates to seisan and sanchin, consider this online article by George Alexander – http://www.worldbudokan.com/Articles/ChinaOriginsWhiteCrane1.htm