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