City Health Commissioner Thomas Frieden also said Tuesday that "many hundreds" of schoolchildren are sick with suspected cases of swine flu.
Bloomberg says the hospitalizations are separate from the outbreak at a private school in Queens.
The mayor says the hospitalized are a child in the Bronx and an adult in Brooklyn.
The U.S. has more than 60 reported cases of swine flu, including 45 in New York City. The sickness has killed dozens in Mexico. Twenty-eight of the 45 New York cases are clustered at St. Francis Preparatory School in Queens -- the largest Catholic High School in the country.
"Thanks to the cooperation of students and staff at St. Francis Preperatory School in Fresh Meadow, Queens, we do however have a much firmer grasp now of the situation at that school," Bloomberg said during a news conference Monday.
"Many family members of these students and staff are also sick," he continued. "We would normally expect to see 1 out of every 5 family members of a person with flu get sick -- and that is exactly what we're seeing with swine flu. And very reassuringly all of the cases have been mild both in students and in staff."
The Associated Press contributed to this report.