You've been a member of Active.com since March of this year, so I will assume you've been running for at least that long. Whether this is something you have been experiencing the whole time, or something that has just started to happen recently, you can benefit from having a gait analysis done by a running store, sports rehab, or physical therapist. It could reveal excess motion in your foot strike that may explain the onset of pain.
Beginning runners gradually build up the muscles that stabilize the ankle. These muscles in the leg attach at various points on the foot via long skinny tendons. These points of attachment can begin to show signs of overuse long after your running routine has begun, but it is more likely when there is excess motion in your running style, or if there has been an abrupt increase in your running distance or intensity. Too much too soon, and chafing or inflammation of these critical structures will become evident.
Another thing to look out for is the stiffening of the muscles controlling your ankle and foot, which will also translate into pain in the ankle as well as occasional pain in the muscles themselves. It can be a sign to back off on your speed or distance, but it also calls for some proactive maintenance. I find the daily shower an ideal time and place to check my leg muscles and work briefly to encourage circulation there. Simply examine the lower leg muscles with soaped fingers for sore spots that may not be felt until pressed this way. Use pressure to glide along the contours of the muscles upwards toward the heart. Examine the nooks and crannies around the bones.
The Peronius (aka Fibularis) muscles are famous for causing front and side ankle pain. These muscles act as stabilizers, plantarflexors, and everters of the foot. Increases in speed, or excess pronation of the foot, are examples of stresses that might contribute to their breakdown. The portions of these muscles that produce ankle pain are found farther up the side of the leg, sometimes just below the knee.
The Tibialis Anterior can be overworked by any action that requires lifting of the toes, which can include climbing hills, or certain footwear. It is important to preventing the toes from dragging, and will often hurt more on a walk than on a run. The pain can appear on the front of the ankle, far from the spot high on the shin where the muscle needs attention.
Check your training regimen and running surface for any changes that can help reduce the load on these muscles while they heal, and make sure your footwear is not too motion-restrictive and has an ample toe box. Meanwhile, scan these muscles for sore spots and work them out with your fingers. If you are in the first year of running, it is normal to hit the wall in your training at some point as you find what your limits are. It is also normal for these problems to work themselves out after the proper attention and adjustments to your schedule.
If the problems continue without relief, you may want to be examined for possible bone and joint structural abnormalities by a podiatrist familiar with the effects of running on the foot. There are many surprisingly common structural variations that can produce excess motion and pain. In many cases, exercise will eventually strengthen your ankle and foot to the point that it won't matter, but getting there can be painful.
Here is a visual aid to help you identify and understand muscles involved in the motion of your ankle:
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