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His own record as the head of the Jesuit order in Argentina at the time has been tarnished as well.
NPR: Argentine Jorge Bergoglio Elected Pope Francis
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Francis, the first pope from the Jesuit order, which is known for its missionary zeal, praised the Colombian saint for "instilling hope" in the indigenous people.
NPR: Pope Francis Gives Church Hundreds Of New Saints
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It was the understated beginning of a papacy that church observers might expect from his Jesuit order, which is known for promoting education and working closely with the poor.
WSJ: New Argentine Pope Faces Church Splits
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Argentina's northern province of Misiones, named for the settlements established during Spanish colonial times by the Catholic Church's Jesuit order, juts like a finger far into Brazil and Paraguay.
WSJ: Bird Watching in Misiones Province, Argentina
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There had been speculation that Pope Francis - who was a member of the Jesuit order - had chosen his name in honour of St Francis Xavier, a 16th Century Jesuit missionary in Asia.
BBC: Pope Francis wants 'poor Church for the poor'
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Instead the cardinals chose this 76-year-old Jesuit whose order is headed by a priest called the superior general, in homage to the military origin of its founder.
BBC: Pope Francis' first moves hint at break with past
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Pope Francis is also the first Jesuit Pope - from an ancient and fiercely independent Catholic order that has not always enjoyed the best relationship with Rome.
BBC: Humble Francis brings both change and continuity
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One unexpected factor is that the new Pope is a Jesuit, a member of perhaps the most powerful and experienced religious order of the Catholic Church.
BBC: Pope Francis quick to stamp his style on papacy
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As a Jesuit, he also carries the strong missionary and educational traditions of that muscular order of priests.
WSJ: Review & Outlook: A Pope From the People
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Yet this Jesuit takes the name Francis from the humble servant of medieval Assisi who began the Franciscan order 300 years before Ignatius.
CNN: Pope Francis, humble, authentic and credible