And the likes of veteran Kees Meeuws and livewire flanker Eben Joubert may be candidates to wear the captain's armband.
Soakai (27) announced this week he was heading to Japan at the end of the Super 15 season, having signed a two-year deal with the Kubota club. He would not play in the ITM Cup for Otago.
He has captained Otago the past two seasons, and though the team has performed poorly, finishing 10th and last in those two seasons, Soakai has been one of the better players.
Mooney said he was realistic about trying to get Soakai to stay.
"I think it is a good time for him now to leave. He has just got married, he has put in the hard yards for Otago and the Highlanders, and has put up some major milestones in the past couple of years," Mooney said.
Soakai brought up 50 caps for Otago last year and will bring up his 50th cap for the Highlanders tomorrow night when the side takes on the Cheetahs at Carisbrook.
Mooney said Soakai was undoubtedly a big loss.
"Not only for the fact that he is an outstanding rugby player but he is a very good leader for the team and will be hard to replace.
"With the World Cup coming up, a whole lot of test players would come on to the market so it would have been harder for Alando to make the move. So I think the timing is good for him."
Mooney said there were candidates to replace Soakai at openside flanker with the likes of contracted players Adam Hill and Eben Joubert, and the newcomer from Wellington, TJ Ioane.
Joubert made a great start to the season last year but it was ended in the Ranfurly Shield challenge when he dislocated his shoulder.
He suffered a severe infection in the shoulder after the operation but has since recovered and should be back playing next month.
Mooney said Joubert had a big opportunity to replace Soakai on the paddock and then step up to fill his boots in the Highlanders.
Joubert also had leadership qualities while former All Black prop Kees Meeuws was available again and could be another captaincy option. Meeuws, who turns 37 in July, captained the team once last year when Soakai was out injured.
