List of number-one Billboard Hot Latin Tracks of 1999
This is a list containing the Billboard Hot Latin Tracks number-ones of 1999.
| Issue date | Song | Artist | Ref. |
| January 2 | "Dejaría Todo" | Chayanne | |
| January 9 | "Dejaría Todo" | Chayanne | |
| January 16 | "Mi PC" | Juan Luis Guerra | |
| January 23 | "Dejaría Todo" | Chayanne | |
| January 30 | "Ese" | Jerry Rivera | |
| February 6 | "Ese" | Jerry Rivera | |
| February 13 | "Ese" | Jerry Rivera | |
| February 20 | "Tú" | Shakira | |
| February 27 | "Ese" | Jerry Rivera | |
| March 6 | "Nunca Te Olvidaré" | Enrique Iglesias | |
| March 13 | "Si Te Pudiera Mentir" | Marco Antonio Solís | |
| March 20 | "Palomita Blanca" | Juan Luis Guerra | |
| March 27 | "No Puedo Olvidar" | MDO | |
| April 3 | "Palomita Blanca" | Juan Luis Guerra | |
| April 10 | "Si Te Pudiera Mentir" | Marco Antonio Solís | |
| April 17 | "Si Te Pudiera Mentir" | Marco Antonio Solís | |
| April 24 | "Livin' La Vida Loca" | Ricky Martin | |
| May 1 | "Livin' La Vida Loca" | Ricky Martin | |
| May 8 | "Livin' La Vida Loca" | Ricky Martin | |
| May 15 | "Livin' La Vida Loca" | Ricky Martin | |
| May 22 | "Livin' La Vida Loca" | Ricky Martin | |
| May 29 | "Livin' La Vida Loca" | Ricky Martin | |
| June 5 | "Livin' La Vida Loca" | Ricky Martin | |
| June 12 | "Livin' La Vida Loca" | Ricky Martin | |
| June 19 | "Livin' La Vida Loca" | Ricky Martin | |
| June 26 | "No Me Ames" | Jennifer Lopez with Marc Anthony | |
| July 3 | "No Me Ames" | Jennifer Lopez with Marc Anthony | |
| July 10 | "Bailamos" | Enrique Iglesias | |
| July 17 | "No Me Ames" | Jennifer Lopez with Marc Anthony | |
| July 24 | "No Me Ames" | Jennifer Lopez with Marc Anthony | |
| July 31 | "No Me Ames" | Jennifer Lopez with Marc Anthony | |
| August 7 | "No Me Ames" | Jennifer Lopez with Marc Anthony | |
| August 14 | "No Me Ames" | Jennifer Lopez with Marc Anthony | |
| August 21 | "Loco" | Alejandro Fernández | |
| August 28 | "De Hoy En Adelante" | Millie | |
| September 4 | "Bella" | Ricky Martin | |
| September 11 | "Bella" | Ricky Martin | |
| September 18 | "Bella" | Ricky Martin | |
| September 25 | "De Hoy En Adelante" | Millie | |
| October 2 | "Dímelo" | Marc Anthony | |
| October 9 | "Dímelo" | Marc Anthony | |
| October 16 | "Dímelo" | Marc Anthony | |
| October 23 | "Dímelo" | Marc Anthony | |
| October 30 | "Dímelo" | Marc Anthony | |
| November 6 | "O Tú O Ninguna" | Luis Miguel | |
| November 13 | "Llegar a Ti" | Jaci Velásquez | |
| November 20 | "Llegar a Ti" | Jaci Velásquez | |
| November 27 | "Llegar a Ti" | Jaci Velásquez | |
| December 4 | "Escúchame" | Carlos Ponce | |
| December 11 | "Ritmo Total" | Enrique Iglesias | |
| December 19 | "Ritmo Total" | Enrique Iglesias | |
| December 25 | "Ritmo Total" | Enrique Iglesias |