The US National Hurricane Center (NHC) said Maria touched down in Yabucoa in the eastern section of the US territory, producing winds of 150 mph (250 km/h).
On the island of Dominica, which was badly hit on Monday, seven people have so far been reported to have been killed.
Aerial footage over the island shows flattened houses and the death toll is likely to rise, because so far information has been hard to come by with communication links still down.
On Tuesday, Maria ploughed through St Croix in the US Virgin Islands, home to around 55,000 people.
Shortly before making landfall in Puerto Rico, the storm was downgraded from category five to category four by the NHC.
Maria was similarly downgraded on Tuesday only to be upgraded again to category five.
Maria is the second storm of this strength to hit the Caribbean this hurricane season - the first being Irma earlier in September.
With the two storm taking a similar track, officials in Puerto Rico fear the debris left by Irma could now prove extremely dangerous in the high winds.
There are also concerns that heavy rain could cause landslides in some places, and that a predicted storm surge of up to 9ft (2.7m) could swamp low-lying areas, with "destructive waves" expected to hit the coast.
The NHC also warned that Maria could deliver several tornadoes over Puerto Rico on Wednesday.
SOURCE: BBC
All feeds
