The answer to your question depends on the situation. With the letters of recommendations, your primary recommender should be your supervisor. Almost all schools will want to hear from this individual with whom you interact frequently and who is responsible for managing you directly and can speak to your development, strengths, and weaknesses.
If you are asking two recommenders from the same company (from a colleague for example), the key will be to ask individuals who can provide different perspectives. For example, in addition to your supervisor, you will ask the individual that you work with cross-functionally on a special project. You won't want to have two recommendations that appear to say the same thing.
Remember that beyond the supervisor, you can select one to two additional recommenders, again from a work setting or potentially from another setting in which you have demonstrated leadership. If you are not sure whether a recommender is appropriate, think about the types of questions they will have to answer. These questions are often frequently linked to your leadership skills, your performance on teams, communication skills, ethics, and more.
I hope this was of help.
Conrad and the Stacy Blackman
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MBA blogger, US News and Author, The MBA Application Roadmap