The Moroccan football federation announced the decision in a statement, the fifth time the North African nation has entered the race to stage the event.
FIFA confirmed those two were the only bids it had received by Friday - the deadline for member associations to officially express an interest in staging the tournament.
Morocco bid unsuccessfully to stage the 1994, 1998, 2006 and 2010 World Cups.
The country was second to the United States in 1994, behind France in 1998 and narrowly lost out to South Africa in its offer to stage the 2010 finals, the only time the tournament has been held in Africa.
"The Royal Moroccan Football Federation has officially submitted its candidacy on Friday, August 11, 2017 to organise the World Cup in 2026,” the statement on the federation's website (www.frmf.ma) said.
"The Federation submitted its application to the relevant committees of the Federation Internationale de Football Association - FIFA - to host this global event."
The 2026 tournament will be the first to be played with 48 teams, making it a huge undertaking for any country.
The Confederation of African Football, which has 54 of FIFA's 211 member national associations, has said it will support the Moroccan bid.
Morocco will be viewed as outsiders to be chosen to host the event. The joint bid by the United States, Canada and Mexico was announced in April.
"We've always been prepared for the fact that other countries could also decide to bid for the 2026 FIFA World Cup," said U.S. soccer federation president Sunil Gulati.
"Competition is good, and overall it shows the value and importance of the World Cup."
Gulati said the North American bid would provide further information next week about which cities were interested in hosting games.
"We'll continue to put together a bid that will meet and exceed the final regulations and specifications required by FIFA," he said.
FIFA said in a statement that the two candidates would have until March to submit detailed bidding documents. The bids will then be evaluated and a report submitted to the FIFA Council.
The final decision will be taken by the full FIFA Congress in Moscow on June 13 next year.
(Writing by Brian Homewood; additional reporting by Simon Evans; Editing by Ken Ferris and Gareth Jones)
