A search began in the sea off Seaford, near Newhaven, when the Coastguard received an alert from the ship’s emergency beacon at about 6am.
A man was found clinging to a buoy and was taken to hospital, the Coastguard said.
Two crew members from the boat, the Joanna C, remain missing and a search is continuing.
The emergency signal put the 45ft scalloping vessel about three nautical miles off the coast.
Two helicopters and two lifeboats were deployed and a coastguard rescue team has been sent to check for sightings from the shore.
Other fishing boats in the area have also been helping with the search.
Piers Stanbury, HM Coastguard controller, said: “Thankfully one of the three people on board at the time of sinking has been pulled out of the water and brought to shore by the Newhaven RNLI lifeboat but the intensive air and sea search for the two missing crew continues.
“Debris has been located close to location of the EPIRB alert location but no life raft has been found as yet.”