WebGL is a JavaScript API for rendering 3D graphics in a web browser without plugins. It is based on OpenGL ES 2.0 and uses the HTML5 Canvas element. Three.js is a popular JavaScript library that makes it easier to use WebGL for 3D graphics. It supports 3D models, materials, textures, lights, and effects. WebGL provides low-level rendering capabilities while Three.js handles complexities like scene graph management, animation, and events.