Autumn leaf colour change happens because chlorophyll — the dominant green pigment — breaks down as days shorten, unmasking the yellow and orange carotenoid pigments that were present all along, while red anthocyanin pigments are often newly produced in autumn itself.

Green chlorophyll is broken down and reabsorbed by the tree before the leaf falls, unmasking carotenoid and tannin pigments that were in the leaf all along — colours the leaf had all summer, just hidden.
This leaf was scanned flat against a plain background for clarity; the pale scanner background itself was excluded from this palette."Autumn American Sycamore Leaf" by Ninjatacoshell, CC BY-SA 3.0, via Wikimedia CommonsA living organism's own chemistry changes with the season — most visibly when a tree stops producing green chlorophyll in autumn, unmasking the yellow, orange and red pigments that were in the leaf all along.
A molecule in the tissue absorbs some wavelengths of light and reflects others — the reflected wavelengths are the colour seen. Chlorophyll, carotenoids and melanin are the most common examples.
Common misconception: Not every vivid natural colour is a pigment — several of the most striking blues and greens in animals are structural colour instead, which looks similar but works completely differently.
As autumn days shorten, deciduous trees stop producing chlorophyll and the existing chlorophyll breaks down, revealing the yellow and orange carotenoid pigments that were present in the leaf throughout the growing season but masked by the stronger green.
Leaves · confidence: high
Unlike carotenoids, red anthocyanin pigments in many species are newly produced in autumn rather than simply unmasked, and their production can be influenced by bright light and cool (but not freezing) temperatures.
Leaves · confidence: high
Many animals show seasonal colour change, most famously species such as the Arctic fox and mountain hare, which moult into white winter coats for camouflage against snow and a browner coat for the snow-free months.
Animals · confidence: high
Flowering and flower colour intensity in many plants follow a seasonal pattern tied to temperature, daylight length and pollinator activity, rather than remaining constant year-round.
Flowers · confidence: medium
Frequency and rarity claims above are scoped to a specific domain, geography or taxonomic group — none are presented as a single universal ranking. See methodology.