List of number-one Billboard Hot Latin Songs of 2006
This is a list containing the Billboard Hot Latin Tracks number-ones of 2006.
| Issue date | Song | Artist |
| January 7 | "Rompe" | Daddy Yankee |
| January 14 | "Rompe" | Daddy Yankee |
| January 21 | "Rompe" | Daddy Yankee |
| January 28 | "Rompe" | Daddy Yankee |
| February 4 | "Rompe" | Daddy Yankee |
| February 11 | "Rompe" | Daddy Yankee |
| February 18 | "Rompe" | Daddy Yankee |
| February 25 | "Rompe" | Daddy Yankee |
| March 4 | "Rompe" | Daddy Yankee |
| March 11 | "Rompe" | Daddy Yankee |
| March 18 | "Rompe" | Daddy Yankee |
| March 25 | "Rompe" | Daddy Yankee |
| April 1 | "Llame Pa' Verte" | Wisin & Yandel |
| April 8 | "Llame Pa' Verte" | Wisin & Yandel |
| April 15 | "Lo Que Son Las Cosas" | Anaís |
| April 22 | "Lo Que Son Las Cosas" | Anaís |
| April 29 | "Lo Que Son Las Cosas" | Anaís |
| May 6 | "Lo Que Son Las Cosas" | Anaís |
| May 13 | "Lo Que Son Las Cosas" | Anaís |
| May 20 | "Lo Que Son Las Cosas" | Anaís |
| May 27 | "Hips Don't Lie" | Shakira featuring Wyclef Jean |
| June 3 | "Hips Don't Lie" | Shakira featuring Wyclef Jean |
| June 10 | "Hips Don't Lie" | Shakira featuring Wyclef Jean |
| June 17 | "Hips Don't Lie" | Shakira featuring Wyclef Jean |
| June 24 | "Hips Don't Lie" | Shakira featuring Wyclef Jean |
| July 1 | "Hips Don't Lie" | Shakira featuring Wyclef Jean |
| July 8 | "Hips Don't Lie" | Shakira featuring Wyclef Jean |
| July 15 | "Hips Don't Lie" | Shakira featuring Wyclef Jean |
| July 22 | "Angelito" | Don Omar |
| July 29 | "Down" | Rakim y Ken-Y |
| August 5 | "Labios Compartidos" | Maná |
| August 12 | "Labios Compartidos" | Maná |
| August 19 | "Labios Compartidos" | Maná |
| August 26 | "Labios Compartidos" | Maná |
| September 2 | "Labios Compartidos" | Maná |
| September 9 | "Labios Compartidos" | Maná |
| September 16 | "Labios Compartidos" | Maná |
| September 23 | "Labios Compartidos" | Maná |
| September 30 | "Ni Una Sola Palabra" | Paulina Rubio |
| October 7 | "Ni Una Sola Palabra" | Paulina Rubio |
| October 14 | "Ni Una Sola Palabra" | Paulina Rubio |
| October 21 | "Ni Una Sola Palabra" | Paulina Rubio |
| October 28 | "¿Quién Me Iba a Decir?" | David Bisbal |
| November 4 | "Pam Pam" | Wisin & Yandel |
| November 11 | "¿Quién Me Iba a Decir?" | David Bisbal |
| November 18 | "¿Quién Me Iba a Decir?" | David Bisbal |
| November 25 | "A la Primera Persona" | Alejandro Sanz |
| December 2 | "Ser o Parecer" | RBD |
| December 9 | "Ser o Parecer" | RBD |
| December 16 | "Bendita Tu Luz" | Maná featuring Juan Luis Guerra |
| December 23 | "Tu Recuerdo" | Ricky Martin featuring La Mari and Tommy Torres |
| December 30 | "Tu Recuerdo" | Ricky Martin featuring La Mari and Tommy Torres |