Hypothesis: Hypothesis is an idea of any scientific observation or phenomenon. Hypothesis form the basis of scientific theory.
Scientific theory: Scientific theory is an idea that has been proven at a fundamental level. A theory is an explanation of a set of related observations or events based upon tested hypotheses and verified multiple times by detached groups of researchers. For example Cell theory.
A scientific hypothesis is a precursor for a scientific theory. Examples of Theories include the Theory of Evolution and the Theory of Relativity. Both have been around in science for a considerable amount of time and are widely accepted in the scientific community to be true. On the other hand hypothesis can be rather new explanations of scientific data. Over time, a hypothesis can be tested and verified and after a substantial amount of evidence has been collected to support the hypothesis and it becomes generally recogonized as the truth, a hypothesis can be upgraded to a Theory.