This study uses historical-critical method. The purpose of this study is to unveil the pedagogy of "pesantren," and at the same time refuting public's assumptions which often have a pejorative view toward "pesantren" as it is regarded as a static institution and a source of radicalism. In fact, as a traditional institution, "pesantren" often shows a positive attitude, flexible and accommodative to any changes. The result of the study shows that "pesantren" has pedagogic concepts that integrate science with art of teaching. There are various methods and strategies of the "pesantren" pedagogy which are still maintained until today, and they can be a model of educational system in the Indonesian "archipelago" as they have contributed to humanity and built peace. In addition, in responding to contemporary issues, "pesantren" has participated in building a democratic society, encouraging awareness of gender equality, improving public service quality, and promoting paradigm shift within "pesantren," i.e. integrative "pesantren."