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It was developed by Dunedin company BrandAid and will be used in all branding for the redeveloped museum.
Museum board chairwoman Dr Dorothy Page said it was a "simple yet elegant" design, that combined the old and new names in an imaginative way and made both elements of the name clearly and equally visible.
"When you consider that we have taken the former museum and redeveloped it into what is effectively a new museum, then this is a very suitable logo."
It reflected the fact the museum was changing and taking a new direction, she said.
"It is a colourful and distinctive branding that we can have some fun with."
She said the size and design of the two elements of the wording complemented each other and provided the elements sought by the museum board and management.
She said "a couple" of Dunedin companies had provided concepts for the logo and a museum advisory board had considered 12 designs before settling on this one. It had cost $4070 in total to arrive at the final design.
The logo would be used on the museum's letterhead, banners, website, advertising and brochures.
Colours used in the design would vary.
Each gallery in the museum had its own colour scheme and there was scope to change the colour used in the logo, to reflect special feature exhibitions, depending on which gallery it was in, she said.
Toitu Otago Settlers Museum will reopen to the public on December 8.