A Mastery is a specialization which will allow ninja to use different techniques that fall under that category. So far there at 8 Masteries to choose from, 5 Elemental and 3 Non-Elemental. Currently you can choose two Masteries, your first at Level 10 and your second at Level 50.
Fire: Fire Elemental Mastery allows the ninja to learn Fire techniques that allow ninjas to dish out large amounts of damage to multiple ninjas.
Wind: Wind Elemental Mastery allows the ninja to learn Wind techniques that are sharp, fast and deadly.
Lightning: Lightning Elemental Mastery allows the ninja to learn Lightning techniques that are high in damage and immobilizing.
Earth: Earth Elemental Mastery allows the ninja to learn Earth techniques that have large area of effect and effectively control crowds.
Water: Water Elemental Mastery allows the ninja to learn Water techniques. Water is a very balanced nature and as such can be useful in many situations.
Medical: Medical Mastery allows the ninja to learn Medical techniques such as healing and reviving fainted ninjas, as well as harness the deadliness of poisons and toxins in combat.
Weapon: Weapon Mastery gives the ninja strong control over tools and blades, making them able to use things like Shurikens, Kunais, Swords in extraordinary ways.
Taijutsu: Taijutsu Mastery allows the ninja to master hand-to-hand combat and learn Taijutsu techniques, taking physical limitations to a new level.