Manuka (Leptospermum, scoparium) smells nicer than ti-tree (Malaleuca alternifolia). It reminds me of the wax-flowers that come from Western Australia.
Ti-tree is highly anti-fungal, and has some anti-viral properties that Manuka doesn't have, but Manuka is an antioxidant and has stronger antibacterial qualities.
Manuka can be a skin irritant, whereas ti-tree is claimed not to be (but I reckon the vapours of Ti-tree can be irritating to eyes if used neat or in a strong solution, like lice treatments and such).
I haven't tested Manuka for it's antifungal properties, but ti-tree is very effective.
(I've read that Manuka is used for muscular treatments, with strong anti-bacterial uses and that both of them can be a problem for pregnant women, in that they are anti-spasmodics, which can be a dangerous thing during childbirth).
I'm not a fan of ti-tree (walking as a child in sand-dune "forests" of ti-tree put me off - their smell was overwhelming and the mass of contorted trees were totally creepy to my child self! - oddly enough, as an adult I like their shape and the papery bark was always fun to play with/draw on/cook with - it makes a great wrap for steaming fish).
Summary? Manuka looks very good on paper, I'd be careful of the skin irritant aspect and suggest you patch test yourself with some diluted oil first to see whether it bothers you. I personally would use a low concentration - the Myrtles tend to have extraordinary "sticking" power in soaps (says me, who's recently acquired, from a grower/processor up north, some Lemon-Myrtle oil [and a few trees] to play with :mrgreen
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