Joel Alama had been fighting for his life in hospital after raising the alarm about the incident which took place on the Oilean an Oir trawler in Killybegs harbour in Donegal on Monday.
His colleague James Joyce, aged 27, originally from Inis Mór in the Aran Islands, died in hospital several hours after being pulled from the trawler’s hold.
Family, friends, and members of the fishing community were attending his funeral on the island as news emerged of the second crew- man’s death.
Mr Alama, aged 46, was originally from General Santos city in the Philippines but had been living on the Aran Islands.
The men were working on the Galway-registered 23m trawler in Killybegs harbour to prepare it for routine engine maintenance when the accident happened.
The boat is owned and operated by the Joyce family and skippered by Mr Joyce’s uncle Stephen.
It is understood that Mr Alama raised the alarm with other crews on the quay after Mr Joyce collapsed before he attempted to rescue him, only to fall ill himself.
Investigations are being carried out by the Marine Casualty Investigation Board and the Health and Safety Authority.
The initial focus of the investigations is on fumes from refrigeration units in the boat’s hold or fumes from stagnant water.
Mr Joyce’s remains were brought to Inis Mór from Rossaveal by the local RNLI lifeboat on Thursday.
His funeral Mass took place in Cill Ronan Church at midday yesterday.
Gardaí confirmed Mr Alama died in Letterkenny General Hospital.