I'd recommend going to your local bike shop and trying on a number of shoes--different shoes will work better with different types of feet. When I went in and bought my first pair of cycling shoes, the bike shop guy looked at my feet and told me I had arches that collapsed if unsupported, which meant I needed a pair of shoes with really good insoles. (I got a pair of Specialized shoes that have great arch support.)
Another think to think about is if you want a road or mountain bike shoe. Mountain bike shoes have recessed cleats (the part that clips in to the pedal), which means that they're much easier to walk around in. Road bike shoes, on the other hand, are a little more streamlined and aerodynamic, and so the cleat sits right on the bottom of the shoe (which makes you walk kind of weirdly in them.) Lots of road bikers (including me!) use mountain shoes because they're easier to walk in and perform almost as well as road shoes, assuming you're not doing any hard core races.
The shoe and pedal brand don't need to be the same (e.g., I have Shimano pedals and Specialized shoes), and while most pedals and shoes are compatible, you should double check when you buy them. It's easiest just to buy them together; that way, you know they're compatible, and the people at the shop can help you install the pedal cleat in your shoes.



? Is it wiser to choose something like Shimano pedals and Shimano shoes since they obviously would be compatible? Is it best to go find the right shoes and then choose the pedals?
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Very well-made shoes, but just not the shape of my foot for long distances.