General synonyms:
* Enigmatic
* Inscrutable
* Puzzling
* Perplexing
* Unfathomable
* Obscure
* Arcane
* Cryptic
* Secret
* Hidden
* Unclear
* Ambiguous
More specific synonyms:
* Intriguing: suggesting a mystery that is captivating or fascinating.
* Eerie: suggesting a mystery that is unsettling or spooky.
* Abstruse: suggesting a mystery that is very difficult to understand.
* Unexplained: suggesting a mystery that is without a clear answer.
* Uncanny: suggesting a mystery that is strange and unsettling.
The best synonym for "mysterious" will depend on the specific context in which you are using the word.