A low similarity percentage might indicate novel species (less likely to be a case) or improper amplification.

Please check if the amplicon size is around 1000 bp or less (700 bp size is generally unacceptable). You could try different universal primers for fungus. You can also go for 28 S instead of 18 S, which will give better results probably. Cross-check similarity with morphological features to get a better idea of the identity of the fungal species. I highly recommend checking the purity of the culture again and go for 18S/28S again.