Cyanocobalamin is the most commonly supplemented form of vitamin B12, but you might be surprised to discover that this form of vitamin B12 does not actually occur in plants or animal tissues. In other words, outside of the chemically synthesized cyanocobalamin that you encounter as B12 in most vitamin supplements, you would be extremely hard pressed to find this compound in nature (in fact you would not be able to find it). As the name implies, cyanocobalamin contains a cyanide molecule. Most people are familiar with cyanide as a poisonous substance. Although the amount of cyanide in a normal B12 supplement is small and from a toxicology point, viewed as insignificant, your body will still need to remove and eliminate this compound. This removal is accomplished through your detoxification systems with substances like glutathione being very important for the elimination of the cyanide.
Compared with cyanocobalamin, it appears that methylcobalamin is better absorbed and retained in higher amounts within your tissues. In simple terms, they are used much more effectively. In general, methylcobalamin is used primarily in your liver, brain and nervous system.