President Pam Whittle said: "The basic problem is because of the similarity of our name with the RHS, people think we're an offshoot of it. We're not. We've always been independent."
She said The Caley was set up to identify the best plants to grow in Scotland and to ensure that the country does not lose its horticultural skills. The society is developing a new base at Saughton Park in Edinburgh, where it has a lottery grant to work on plans for an application for a full grant in August 2015.
"If I change the title to 'The Caley', using the RCHS subtitle because it's a royal charter, I'll have to be very careful. It's important because the Queen Mother had a long, association with us.
"But with the independence vote, organisations in Scotland are becoming aware of the need to have a national identity and profile. Scotland needs to think about its own identity in horticultural terms rather than being part of a region. To be a national society you have to be seen to be giving something to all of the communities and with the geography of Scotland that's quite a challenge.
"The RHS can't do that and that's why their focus is on schools. We don't want to compete with them - we want to do what's needed."