| Competition: | Liga Nacional |
| Season: | 1999–2000 |
| Winners: | Apertura: Motagua Clausura: Motagua |
| Relegated: | Federal |
| Continentalcup1: | Copa Interclubes UNCAF |
| Continentalcup1 Qualifiers: | Motagua Olimpia |
| League Topscorer: | Apertura: Wilmer Velásquez (12) Clausura: Juan Cárcamo (14) |
| Total Goals: | 507 |
| Matches: | 204 |
| Biggest Home Win: | Platense 8–0 Universidad (10 June 2000) |
| Biggest Away Win: | Federal 2–7 Motagua (10 October 1999) |
| Highest Scoring: | Motagua 8–2 Vida (30 September 1999) |
| Prevseason: | 1998–99 |
| Nextseason: | 2000–01 |
| Updated: | 26 August 2000 |
The 1999–2000 Honduran Liga Nacional was the 35th season in the Honduran top division, the tournament was divided into two halves (Apertura and Clausura) and it determined the 35th and 36th national champions in the league's history. The league games started 18 September 1999.[1]
The Apertura was the opening half of 1999–2000 season in the Honduran Liga Nacional.
As of 22 December 1999
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The Clausura tournament of the 1999–2000 season in the Liga Nacional de Fútbol de Honduras started on 11 March 2000 at San Pedro Sula with a scoreless match between C.D. Marathón and C.D. Platense.
As of 2 July 2000
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Note: Motagua (3rd) had the right to play the second leg at home after finishing above Marathón (5th) in the regular season; Marathón however claimed they had to close the series at home after they defeated Platense in the Hexagonal who finished 2nd; eventually Motagua granted home-field advantage in the second leg at San Pedro Sula.[3]
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| GK | – |  Carlos Prono | ||
| RB | – | Rudy Williams | ||
| CB | – | Gregorio Serrano | ||
| CB | – | Merlyn Membreño | ||
| LB | – | Samuel Caballero | ||
| CM | – | Cristian Santamaría | ||
| CM | – | José Pineda | ||
| CM | – | Alex Pineda | ||
| AM | – | Danilo Tosello | ||
| CF | – |  Denilson Costa | ||
| CF | – | Wilmer Velásquez | ||
| Substitutions: | ||||
| FW | – | |||
| MF | – | |||
| MF | – | |||
| Manager: | ||||
| Julio González | ||||
| GK | – | Diego Vásquez | ||
| RB | – | Jorge Lozano | ||
| CB | – | Reynaldo Clavasquín | ||
| CB | – | Elmer Montoya | ||
| LB | – | Iván Guerrero | ||
| CM | – | Oscar Lagos | ||
| CM | – | Mario Chirinos | ||
| AM | – | Amado Guevara | ||
| RF | – | Francisco Ramírez | ||
| CF | – | Gustavo Fuentes | ||
| LF | – | Jairo Martínez | ||
| Substitutions: | ||||
| GK | – | |||
| MF | – | |||
| FW | – | |||
| Manager: | ||||
| Luis Reyes | ||||
Relegation was determined by the aggregate table of both Apertura and Clausura tournaments.
| Broncos | ||||
|---|---|---|---|---|
| Juan Ramón Palacios | Edgar Figueroa | Luis Oseguera | ||
| Marco Ortega | Jorge Pineda | César Méndez | ||
| Marcelo Ferreira Martins | José Villatoro | Nelson Rosales | ||
| Luis Vallejo | José Suazo | |||
| Federal | ||||
| Héctor Medina | Presley Carson | Orlando Rene López | ||
| Walter "Gualala" Trejo | César Colón | Jorge "Avioneta" Martínez | ||
| Marvin Fonseca | Miguel Arcángel Güity |  Harold Yepes | ||
| Jose "Chepo" Fernández | Carlos Pérez | Ricardo Correa | ||
| Luis Ronaldo Bernardo | Rony Zelaya | Marvin Brown | ||
| Marathón | ||||
| Josué Reyes | Hernaín Arzú | Jesús Romero | ||
| Edwin Medina | Maynor Suazo | Silvio Rudman | ||
| Douglas Murillo | Carlos Lemus | Carlos González | ||
| Alejandro Naif | Gerardo Aguilar | Marvin Brown | ||
| Darwin Pacheco | Pompilio Cacho Valerio | Sebastián Rudman | ||
| Nigel Zúniga | Mauricio Sabillón | Behiker Bustillo | ||
| Luis Guifarro | Jaime Rosales | José Luis López Escobar | ||
| Narciso Fernández | ||||
| Motagua | ||||
| Diego Martin Vásquez | Júnior Izaguirre | Ninrrod Medina | ||
| Amado "El Lobo" Guevara | Hugo Caballero | Reynaldo Clavasquín | ||
| Robel Bernárdez | Juan Carlos Raudales | Carlos "Pony" Muñoz | ||
| Ramón Romero "Romerito" | Iván Guerrero | Mario Chirinos | ||
| Jairo "Kiki" Martínez | Gustavo Fuentes | Milton "Jocon" Reyes | ||
| Oscar "Chicano" Lagos | Carlos Alberto Salinas | Juan Moles | ||
| Roberto "Tanque" Rojas | José Francisco Ramírez | |||
| Olimpia | ||||
| Wilmer Velásquez | Carlos Prono | Marlon Hernández | ||
| Alex Pineda Chacón | Nahúm Espinoza | Elmer Marín | ||
| Merlyn Membreño | Rodinei Martins | Enrique Reneau | ||
| Samuel Caballero | Danilo Tosello | Christian Santamaría | ||
| Platense | ||||
 Ricardo James | Marco Mejía | José Luis Piota | ||
| Marcio Machado de Lima | Julio César De León | Hernán Centeno | ||
| Rubén Suazo | Juan Manuel Cárcamo | |||
| Real España | ||||
| Milton "Chocolate" Flores | Wilmer "Superman" Cruz | Víctor Carneiro | ||
| Marlon Hernández | Leonardo Morales | Miguel Mariano | ||
| Luis "Bombero" Ramírez | Reynaldo "Chino" Pineda | Edgar Rolando Delgado | ||
| Washington "Piojo" Hernández | Jorge Zapata | Marco "Chacal" Ortega | ||
| Ricky Garcia | Leonardo "Leo" Isaula | Leonardo "Leo" Morales | ||
| David Cárcamo | Hector Gutiérrez | Mario "Pescado Rodríguez | ||
| Javier Rodríguez | Carlos Oliva | Orbin "Pato" Cabrera | ||
| Cesar "Nene" Obando | ||||
| UNAH | ||||
| Constantino Reyes | Hesler Phillips | José Luis "Runga" Piota | ||
| Silvio Traverso | Cristian González | Carlos Daniel Díaz | ||
| Juan Carlos González | Guillermo Sumich | Leonel Rodríguez | ||
| Elvis Danilo (Dany) Turcios | Aminadan Laines | Luis Perdomo | ||
| Juan Rosa Lagos | Camilo Bonilla Ocampo | Marvin Mazariegos | ||
| Jorge Arita Neal | Ricky Alcerro | Raul Dolmo | ||
| Victoria | ||||
| Eugenio Dolmo Flores | Carlos Alberto Escobar | Héctor Zapata | ||
| Julio César Suazo | Renán Bengoché | Luis Perdomo | ||
| Guillermo Ramírez | Héctor Fernández | Luis Ramos | ||
| Nicolás Suazo | Marcos Bernárdez | Hernán Fúnez | ||
| Luis Lagos | Mauricio Figueroa | Cristian Martínez | ||
| Enrique Reneau | Jorge Pineda | |||
| Vida | ||||
| Wilmer Cruz | Carlos Alvarado | Geovanny Arzú | ||
| Roberto Padilla | Renán Contreras | Clayd Marson | ||
| Jorge Ocampo | Francis Javier Reyes | Marlon Monge | ||
| René Martínez | Alberto Zapata | José Pacini | ||