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The purpose of this study is to investigate whether two English prefixes dis- and un- exhibit different phonological distributions, and to formalize the tendency and motivation by stochastic phonological theory. For this purpose, this study collects the data from Carnegie Mellon University Pronouncing Dictionary and analyses them by conducting a series of simple linear regression tests. As a result, our finding is that the distribution of dis- and un- is different with each other depending on the initial stops(both oral and nasal) and liquids of the bases they attach. By formalizing the distribution within the framework of Maximum Entropy Grammar(Maxent; Hayes and Wilson 2008), we can identify that the interaction of the phonological motivations like voice assimilation, obligatory contour principle, syllable contact law and other English phonotactics affects the distribution. Thus, dis- is more likely to attach to base-initial voiceless stops, while un- tends toward voiced stops, nasal [n], and liquids. Furthermore, we conduct a survey experiment of English native speakers to confirm the prediction of the Maxent grammar. The result is that the tendency predicted by the grammar largely reflects the intuition of English native speakers.