Ever since the inception of generative linguistics, various dependency patterns have been widely discussed in the literature, particularly as they pertain to the hierarchy based on “weak generation” – the so-called Chomsky Hierarchy. However, humans can make any possible dependency patterns by using artificial means on a sequence of symbols (e.g., computer programing). The differences between sentences in human language and general symbol sequences have been routinely observed, but the question as to why such differences exist has barely been raised. Here, we address this problem and propose a theoretical explanation in terms of a new concept of “Merge-generability,” that is, whether the structural basis for a given dependency is provided by the fundamental operation Merge. In our functional magnetic resonance imaging (fMRI) study, we tested the judgments of noun phrase (NP)-predicate (Pred) pairings in sentences of Japanese, an SOV language that allows natural, unbounded nesting configurations. We further introduced two pseudo-adverbs, which artificially force dependencies that do not conform to structures generated by Merge, i.e., non-Merge-generable; these adverbs enable us to manipulate Merge-generability (Natural or Artificial). By employing this novel paradigm, we obtained the following results. Firstly, the behavioral data clearly showed that an NP-Pred matching task became more demanding under the Artificial conditions than under the Natural conditions, reflecting cognitive loads that could be covaried with the increased number of words. Secondly, localized activation in the left frontal cortex, as well as in the left middle temporal gyrus and angular gyrus, was observed for the [Natural – Artificial] contrast, indicating specialization of these left regions in syntactic processing. Any activation due to task difficulty was completely excluded from activations in these regions, because the Natural conditions were always easier than the Artificial ones. And finally, the [Artificial – Natural] contrast resulted in the dorsal portion of the left frontal cortex, together with wide-spread regions required for general cognitive demands. These results indicate that Merge-generable sentences are processed in these specific regions in contrast to non-Merge-generable sentences, demonstrating that Merge is indeed a fundamental operation, which comes into play especially under the Natural conditions.