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This study traces the evolution of imperial science in the Zamboanga Peninsula through three major scientific expeditions: the Spanish Malaspina Expedition (1792), the British survey of H.M.S. Samarang (c. 1844), and the American collecting expeditions of Joseph Beal Steere (1874, 1887). By examining their reports, drawings, and specimen lists, the paper reconstructs how each mission’s scientific purpose, method, and institutional backing reflected successive phases in the history of colonial knowledge. Alejandro Malaspina’s 1792 visit to Zamboanga formed part of a global Spanish imperial survey aimed at assessing the empire’s resources and producing a visual and cartographic inventory of its possessions. Half a century later, Frank Marryat, a midshipman aboard H.M.S. Samarang, approached Zamboanga within the British tradition of hydrographic survey and travel literature. By the late nineteenth century, Joseph Beal Steere’s expeditions marked a decisive shift toward professional, university-based science. Funded by the University of Michigan, Steere’s work reduced the landscape to catalogues of species, reflecting the commodification of nature as data. Across these missions, Zamboanga served as subject and constraint. Its geography—a narrow coastal plain bounded by forested highlands—and its status as a fortified frontier shaped what could be seen, collected, and recorded. Each expedition produced knowledge filtered through local conditions of danger, accessibility, and order. Collectively, their archives chart a century-long transformation in the practice of imperial science: from state-sponsored Enlightenment survey to the rise of institutionalized academic natural history.