According to www.ultracycling.com, the primary muscles used in biking are the gluteal muscles, quadriceps, hamstrings and calf muscles. The quadriceps are the large muscles on the front of the thigh that are responsible for straightening the leg and pushing the pedal down towards the ground. The gluteus maximus and medius are located in your buttocks and are responsible for pushing the pedal forward at the top of the stroke. The hamstrings are located on the back of the thigh, and they work with the calf muscle to lift the pedal up from the bottom of the stroke. All of these muscles work together to give you power when pedaling and endurance when riding.
The type of riding you do will use some of these muscles more than others. If the terrain is hilly, the quadriceps will do more of the work powering up the hills. When standing to get up a hill, the gluteal muscles will be more engaged. Speed work or riding against the wind will engage all of the leg muscles more.
Other muscles outside of the legs are used as supporting muscles when riding. Depending on the terrain and the handlebars used, upper body muscles will be engaged. This happens when standing to climb a hill and pulling up on the handlebars to get more power, which uses the bicep muscles. When using aerobars and resting your upper body on them while riding, the tricep muscles, located on the back of the upper arm, will be used to support your body weight. Also, to a lesser extent, the muscles in the back and abdominal region are used for stabilization while on the bike.
Biking has many physical benefits. If it is done frequently and with enough intensity, it will help you burn calories, lose fat, improve heart and lung functioning and work major muscles throughout your body. Muscles will respond by getting stronger, resulting in a body that is leaner, fitter and has more stamina.