Reference manual & Datasheet
The datasheet for a microcontroller generaly covers the specific details about a single chip, or a closely-related group of chips. It contains things like pinouts, specific I/O features, and the performance data.

On the other hand, the reference manual generally goes into a lot more depth on all of the features associated with an entire family of chips, generally chips that share a common CPU architecture. It contains programming information for both the CPU and all of the peripherals that chips in the family might contain.

When the two sources contain overlapping information &mdash; and they don't agree &mdash; it can be difficult to determine which one is authoritative. Look at dates published, look for errata documents, talk to FAEs, etc.