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| First Round Draft Pick History |
| Complete Draft History |
| 2 | 12 | 36 | 2016 | Annual Draft | SP | Tommy | Milone | MLB |
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| 3 | 12 | 60 | 2016 | Annual Draft | RP | Matt | Albers | MLB |
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| 4 | 14 | 86 | 2016 | Annual Draft | RP | Fernando | Rodriguez | MLB |
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| 5 | 14 | 110 | 2016 | Annual Draft | RP | Antonio | Bastardo | MLB |
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| 6 | 14 | 134 | 2016 | Annual Draft | C | Tony | Cruz | MLB |
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| 8 | 12 | 180 | 2016 | Annual Draft | SP | Felix | Doubront | MLB |
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| 9 | 13 | 205 | 2016 | Annual Draft | SP | Tyler | Cravy | MLB |
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| 10 | 12 | 228 | 2016 | Annual Draft | SP | Chris | Capuano | MLB |
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| 10 | 14 | 230 | 2016 | Annual Draft | RP | Blake | Treinen | MLB |
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| 11 | 12 | 252 | 2016 | Annual Draft | SP | Yohan | Flande | MLB |
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| 11 | 14 | 254 | 2016 | Annual Draft | SP | Jerome | Williams | MLB |
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| 13 | 12 | 300 | 2016 | Annual Draft | C | Bobby | Wilson | MLB |
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| 14 | 14 | 326 | 2016 | Annual Draft | OF | Kyle | Parker | MLB |
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| 15 | 12 | 348 | 2016 | Annual Draft | RP | Jason | Motte | MLB |
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| 16 | 14 | 374 | 2016 | Annual Draft | SP | Sean | O'Sullivan | MLB |
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