Staffordshire bull terrier Jodie, 12, has both male and female reproductive organs and was found abandoned in Essex three months ago.
The RSPCA believes the condition could be the reason it was given up by her previous owner and may be putting people off rehoming her.
Hermaphroditism is very rare in dogs, the charity added.
Jodie was rescued by the RSPCA in Southend in October and staff at the charity's Essex branch soon discovered the unusual condition.
Read more Essex stories here
Dog co-ordinator Kathy Butler said: "Jodie has been with us for a number of months now and we haven't had a single inquiry for her. It's such a shame because she is a lovely little dog.
"As an older Staffie with an unusual physicality, we think Jodie is being unfairly overlooked."
While the condition is common in some animals, the RSPCA's London veterinary director Caroline Allen said the phenomenon is "very rare" in dogs, although it is not thought to cause any problems.
"I've never seen a case in 19 years of practice," she said.
An "unwanted and unloved" dog is struggling to find a new home because it is a hermaphrodite, the RSPCA said.