Bowen, who was surprisingly sacked from his role as Steve Bruce's right-hand man in the summer, has teamed up with the former Wales boss who replaced Graeme Souness as manager of Rovers earlier this week.
The former Blues first team coach rejoined the Wales international coaching staff after a two year absence at the beginning of August and both he and Hughes will take charge of their next two 2006 World Cup qualifiers against England and Poland next month despite their appointments at Ewood Park.