Botwoon is an aquatic serpentine creature tasked with guarding the approach to Draygon in the depths of Maridia. When it is encountered, it employs hit and run tactics, ramming and spitting objects at Samus before retreating into one of several holes in the back wall of the chamber. Its movements are very erratic, and as such can be difficult to predict.
The best way to kill him is to fire missiles or super missiles at his head. While the charge beam will also work, it can be difficult to line up the shot, especially in the later stages of the fight when it is moving extremely quickly. After its defeat, Samus can continue her exploration of Maridia.
The tactics needed to defeat it are somewhat similar to those needed to combat Serris in Metroid Fusion