This research aims to reveal whether Japanese EFL (English as a foreign language) learners correctly understand the meanings of the English basic discourse markers but and so. In Study 1, 407 Japanese university students were requested to judge whether each of the meanings of 31 Japanese discourse markers could be expressed with but/so. In Study 2, 302 Japanese university students were requested to read ten Japanese passages including a blank each and judge whether but/so is appropriate for each blank. Also, 11 English native speakers were requested to read ten English passages including a blank each and answer what words are appropriate for each blank. The results of the analyses of their judgements and answers showed that (a) Japanese EFL learners understand that but can express the adversative relationship, which is almost the same as English native speakers’, (b) Japanese EFL learners understand that so can express some relationships including the causal one, the range of which is wider than that for English native speakers. This research suggested that so is more difficult to acquire for Japanese EFL learners, and therefore they are required to have instruction in the meanings of so.