# Hypocotyl

> The section of seedling stem between the root and the cotyledons; it elongates to lift the seed leaves above the medium.

- Canonical: https://genetixbay.com/knowledge/glossary/hypocotyl.html
- Also written: seedling stem, hypocotyl stem, stem below the cotyledons
- Glossary category: Plant biology · Evidence: Established
- Status: Draft: awaiting expert review · Updated: 2026-10-31
- Licence: CC BY-SA 4.0 (https://creativecommons.org/licenses/by-sa/4.0/), attribute "GenetixBay cannabis glossary"

The hypocotyl is the part of the embryonic axis below the [cotyledons](https://genetixbay.com/knowledge/glossary/cotyledon.md) and above the root. After the [radicle](https://genetixbay.com/knowledge/glossary/radicle.md) emerges, the hypocotyl lengthens in a hook shape, pushes up through the medium, then straightens to raise the cotyledons into the light. Its length is controlled largely by light signals perceived by [phytochromes](https://genetixbay.com/knowledge/glossary/phytochrome.md) and cryptochromes.

## In practice

A long, thin, floppy hypocotyl is the classic "stretched [seedling](https://genetixbay.com/knowledge/glossary/seedling.md)". It means too little light (or too little blue, or a lamp much too far away), sometimes combined with heat. Seedlings typically do fine around 100-300 [µmol/m²/s](https://genetixbay.com/knowledge/glossary/ppfd.md) at canopy; very dim windowsills give leggy hypocotyls.

Growers often bury a stretched hypocotyl deeper at transplant. Cannabis can root along a buried stem, and the plant gains support. Keep the cotyledons above the surface.

The hypocotyl is also the tissue most attacked by [damping-off](https://genetixbay.com/knowledge/glossary/damping-off.md) fungi, which pinch it at the soil line.

## Don't confuse with

- **Epicotyl**: the stem above the cotyledons, carrying the [first true leaves](https://genetixbay.com/knowledge/glossary/true-leaves.md).
- **Internode**: the stem length between two nodes on an established plant.
- **Radicle**: the embryonic root below it.

## Related terms

[Cotyledon](https://genetixbay.com/knowledge/glossary/cotyledon.md), [Radicle](https://genetixbay.com/knowledge/glossary/radicle.md), [True leaves](https://genetixbay.com/knowledge/glossary/true-leaves.md), [Phytochrome](https://genetixbay.com/knowledge/glossary/phytochrome.md)

## Read more

- [Seedling care: the first three weeks](https://genetixbay.com/knowledge/germination/seedling-care.md)
- [Stretchy, leggy cannabis: a differential](https://genetixbay.com/knowledge/diagnosis/stretching.md)

## Sources

1. Taiz L, Zeiger E, Møller IM, Murphy A. 2015. Plant Physiology and Development, 6th edition. Sinauer Associates.