For the first – and to date only – time, Hughes entered the 24 Hours of Daytona in 2006; driving a Cheever Racing-entered Crawford DP03-Lexus alongside Stefan Johansson and Thomas Erdos, and finishing 22nd overall. Hughes remained with Team LNT for that year's Le Mans Series, now driving a GT2-class Panoz Esperante GTLM. The season started poorly, with Hughes, partnered with Robert Bell, retiring from the 1000 km of Istanbul. The 1000 km of Spa proved to be equally unsuccessful, with Hughes retiring once more. Following these two races, Hughes competed in the 24 Hours of Le Mans for ASM Team Racing, alongside Miguel Amaral and Miguel Ángel de Castro, driving a Lola B05/40-AER, but once more without success; retiring due to gearbox failure after 196 laps. His first finish of the season, a tenth class placing, came at the 1000 km of Nürburgring, before finishing the season by winning the two remaining events of the season (the 1000 km of Donington and the 1000 km of Jarama). These two victories were enough to allow Hughes and Bell's No.81 Panoz to finish third in the championship, one point and one place behind the No.82 Panoz of fellow Team LNT members Tomlinson and Dean, with Team LNT finishing second, one point behind Autorlando Sport.