They are very different. There is only a very slight overlap, certainly, but that overlap on this site is only about the practical implementation of cryptography. From our faq:
IT Security Stack Exchange is for Information Security professionals to discuss protecting assets from threats and vulnerabilities. Topics include, but are not limited to:
- web app hardening
- network security
- social engineering, including phishing
- risk management
- penetration testing
- security tools
- using cryptography
- incident response
- physically securing the office, datacentre, information assets etc.
Questions on setting up your home PC antivirus may be more appropriate over at superuser.com; and questions on the deeper aspects of cryptography belong on crypto.SE.
and from the Crypto faq:
Crypto Stack Exchange is for software developers, mathematicians and others interested in cryptography.
Cryptography Stack Exchange is for asking questions about the mathematics and properties of cryptographic systems, their analysis ("cryptanalysis") and subsidiary topics that generally make up cryptology, such as random number generation. As such, we welcome questions on topics such as:
- Asymmetric and symmetric cryptographic algorithms.
- Cryptographic protocols.
- Cryptanalysis techniques.
- Hash functions, hashing.
- Entropy and information theory.
- Random number generation.
Here we don't worry about the algorithms, or the mathematics, or theoretical attacks on a set - we are focused on what those attacks might do to the enterprise we are trying to protect.
So if your question is about cryptography, in almost all cases you should ask on Cryptography.SE - the exceptions are when it comes to practical implementation, and then your question may be on topic here.