His case involved the deaths of 39 people found in the back of a container truck in an industrial park on October 23 in the English town of Grays.
The 40-year-old of County Armagh in Northern Ireland agreed to enter the plea at Central London Criminal Court.
All of the victims of Britain’s human smuggling case were all Vietnamese.
The scope of the tragedy became clear as police released the names and ages of those who died in one of Britain’s worst incidents of human smuggling.
Two of the dead were only 15, while the oldest was 44. About 20 of the victims came from one province, Nghe An, in north-central Vietnam.
Hughes also pleaded guilty to conspiracy to assist unlawful immigration of non-European Union citizens between May 1, 2018 and October 24, 2019.
Hughes appeared alongside Eamonn Harrison, 23, also of County Down, Northern Ireland, who is alleged to have driven the truck's trailer to the Belgian port of Zeebrugge before it sailed to Purfleet in England.
Harrison pleaded innocent to 39 counts of manslaughter and one count of conspiracy to assist unlawful immigration and will face trial October 5 with three others.
Gazmir Nuzi, 42, of Tottenham in north London, who appeared via video-link, pleaded guilty to a single charge of assisting unlawful immigration on or before October 11, 2019 and April 18, 2020.
The pleas were not the first in the tragic case.
Another driver Maurice Robinson, 25, of Craigavon in Northern Ireland pleaded guilty to 39 counts of manslaughter in April.
Robinson discovered the bodies after transporting the container from Purfleet to Grays.
In June, Alexandru-Ovidiu Hanga, 28 admitted to one count of conspiring to assist unlawful immigration.
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