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Western Conference
Eastern Conference
Promotion ~ USL (Play Offs: )
1/8-finals
Quarter-finals
Semi-finals
Final
2016 Main
Western Conference
| Pl | W | D | L | Diff | Pts | |||
| 1 | Sacramento Republic | 30 | 14 | 10 | 6 | 43:27 | 16 | 52 |
| 2 | Rio Grande | 30 | 14 | 9 | 7 | 47:24 | 23 | 51 |
| 3 | Colorado Springs | 30 | 14 | 7 | 9 | 37:27 | 10 | 49 |
| 4 | Sporting Kansas City II | 30 | 14 | 6 | 10 | 45:36 | 9 | 48 |
| 5 | LA Galaxy 2 | 30 | 12 | 11 | 7 | 52:42 | 10 | 47 |
| 6 | Vancouver Whitecaps 2 | 30 | 12 | 9 | 9 | 44:44 | 0 | 45 |
| 7 | Oklahoma City Energy | 30 | 10 | 13 | 7 | 32:30 | 2 | 43 |
| 8 | Orange County SC | 30 | 12 | 4 | 14 | 39:41 | -2 | 40 |
| 9 | Portland Timbers 2 | 30 | 12 | 4 | 14 | 38:42 | -4 | 40 |
| 10 | San Antonio | 30 | 10 | 8 | 12 | 36:36 | 0 | 38 |
| 11 | Real Monarchs | 30 | 10 | 6 | 14 | 31:41 | -10 | 36 |
| 12 | Tacoma Defiance | 30 | 9 | 8 | 13 | 35:50 | -15 | 35 |
| 13 | Arizona United | 30 | 9 | 7 | 14 | 40:46 | -6 | 34 |
| 14 | Saint Louis FC | 30 | 8 | 10 | 12 | 42:44 | -2 | 34 |
| 15 | FC Tulsa | 30 | 5 | 4 | 21 | 25:64 | -39 | 19 |
Eastern Conference
| Pl | W | D | L | Diff | Pts | |||
| 1 | New York Red Bulls 2 | 30 | 21 | 6 | 3 | 61:21 | 40 | 69 |
| 2 | Louisville City | 30 | 17 | 9 | 4 | 52:27 | 25 | 60 |
| 3 | FC Cincinnati | 30 | 16 | 8 | 6 | 41:27 | 14 | 56 |
| 4 | Rochester New York | 30 | 13 | 12 | 5 | 38:25 | 13 | 51 |
| 5 | Charlotte Independ | 30 | 14 | 8 | 8 | 48:29 | 19 | 50 |
| 6 | Charleston | 30 | 13 | 9 | 8 | 38:33 | 5 | 48 |
| 7 | Richmond Kickers | 30 | 12 | 9 | 9 | 33:26 | 7 | 45 |
| 8 | Orlando City B | 30 | 9 | 8 | 13 | 35:49 | -14 | 35 |
| 9 | Wilmington Hammerheads | 30 | 8 | 10 | 12 | 37:47 | -10 | 34 |
| 10 | Penn | 30 | 8 | 7 | 15 | 37:54 | -17 | 31 |
| 11 | Bethlehem | 30 | 6 | 10 | 14 | 32:43 | -11 | 28 |
| 12 | Toronto FC II | 30 | 7 | 5 | 18 | 36:58 | -22 | 26 |
| 13 | Pittsburgh | 30 | 6 | 7 | 17 | 31:50 | -19 | 25 |
| 14 | FC Montreal | 30 | 7 | 2 | 21 | 35:57 | -22 | 23 |
Promotion ~ USL (Play Offs: )
2016 Play Offs
1/8-finals
| 1 | New York Red Bulls 2 | Orlando City B | 4 : 0 |
| 2 | Charlotte Independ. | Rochester New York | 1 : 3 |
| 3 | Charleston | FC Cincinnati | 2 : 1 |
| 4 | Richmond Kickers | Louisville City | 0 : 2 |
| 5 | Sporting Kansas City II | LA Galaxy 2 | 3 : 0 |
| 6 | Sacramento Republic | Orange County SC | 0 : 1 |
| 7 | Oklahoma City Energy | Rio Grande | 3 : 2 |
| 8 | Colorado Springs | Vancouver Whitecaps 2 | 1 : 2 |
Quarter-finals
| 1 | New York Red Bulls 2 | Rochester New York | 4 : 3 |
| 2 | Charleston | Louisville City | 0 : 1 |
| 3 | Sporting Kansas City II | Orange County SC | 2 : 1 |
| 4 | Oklahoma City Energy | Vancouver Whitecaps 2 | 2 : 3 |
Semi-finals
| 1 | New York Red Bulls 2 | Louisville City | 2 : 1 |
| 2 | Sporting Kansas City II | Vancouver Whitecaps 2 | 3 : 0 |
Final
| 1 | New York Red Bulls 2 | Sporting Kansas City II | 5 : 1 |
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