Both “masen” and “naidesu” are the polite negative ending forms of a Japanese sentence. However, native speakers of Japanese will adjust accordingly between the two words depending on formality, part of speech used and medium chosen. Nonetheless, differences in usage are hardly taught in the classroom. Moreover, Japanese textbooks for learners usually introduce one of the two forms in each part of speech. From this, a question arises: How do Japanese learners distinguish between these two forms? This research investigates the different usages of the two Japanese negative forms “masen” and “naidesu” by Japanese learners. Advanced-level Japanese learners in Japan were asked to fill in the blanks of two questionnaires. The setting was to write an email to their teacher and a senior who was one year older than themselves respectively. The results show that learners tend to make different use of the two forms with regard to hierarchal relations with whom they write to and the part of speech conjugated just like native speakers of Japanese. However, some learners only wrote “naidesu” after I-adjectives, while some others did not seem to use the two forms separately according to hierarchal relations. The results indicate that those learners did not have a definite distinction between the two forms unlike Japanese natives. Previous research has indicated that Japanese natives use “naidesu” frequently in spoken language, especially with I-adjectives. This research, on the other hand, shows that the natives avoid “naidesu” even with I-adjectives when they write emails to their seniors. In conclusion, the importance to teach Japanese learners the difference in usage between “masen” and “naidesu” is asserted in this research.