In both instances, the bomb squad was called out and portions of the four-story duPont Center where the offices are located were evacuated.
The substance in the letter sent to Rubio, a Republican, turned out to be corn starch, the Fire Department said.
There was no word on the identity of the substance contained in Democrat Nelson's letter, but the FBI said it was harmless.
FBI spokesman Jeff Westcott said the agency's Jacksonville office has opened an investigation into the two mailings.
"We don't know that they are connected for sure," he said. "There certainly are similarities."