The first limb was found around 8:20 a.m. Wednesday in roughly the same spot where the men's boat capsized.
Around 1 p.m. Thursday, authorities searching the area found a second leg, according to Aaron Belda of the Palos Verdes Estates Police Department. An unconfirmed human femur was also discovered, according to Belda.
Investigators are now trying to determine if they have any connection to the two missing men. The Los Angeles County Medical Examiner will investigate the remains to assess its possible connection to them.
The missing boaters launched from the Cabrillo Marina on Monday but never returned. Crews began a search Tuesday morning and found a boat up against the rocks near the 1800 block of Paseo Del Mar but the men were not found.
The search resumed Wednesday morning. However, in an update at 1:41 p.m. Wednesday, the Coast Guard announced the search was called off due to "no signs of distress" and "no response to UMIB (Urgent Marine Information Broadcast)."
Coast Guard suspends search for 2 missing boaters off coast of Palos Verdes Estates
The two men's names have not been released but authorities described them as being in their 50s.
Authorities had warned the public to stay out of the water at Southland beaches Tuesday and Wednesday due to large waves and dangerous rip currents. A high surf advisory was issued by the National Weather Service that continued until 9 p.m. Wednesday for Los Angeles County beaches.
Forecasters said "large breaking waves" of 8 to 13 feet impacted west-facing beaches Tuesday morning.
City News Service Inc. contributed to this report.