Bean fly (bean stem maggot)

Ophiomyia phaseoli Ophiomyia phaseoli (Tryon, 1895) · formerly or also: Agromyza phaseoli, Melanagromyza phaseoli

bean stem maggot · English, Africa
French bean fly · English, Asia and Oceania (older literature)
inzi wa maharage · Swahili, East Africa

The bean fly is a tiny shiny black fly whose maggots tunnel down from the leaves into the stems of young bean plants. They feed just under the skin at the base of the stem, which swells and cracks, so seedlings yellow, wilt and die. It is one of the most damaging pests of common bean and other legumes on small farms in Africa and Asia, especially when beans are planted into dry or poor soils. In Africa two related species, Ophiomyia spencerella and O. centrosematis, cause the same damage.

Adult male bean fly (Ophiomyia phaseoli), a tiny dark fly, magnified. Photo: Lonsdale O, Murphy ST, Scheffer SJ, CC BY 4.0, via Wikimedia Commons.

Type: Insect · Insect (small fly; the maggots tunnel in stems)
Classification: Animalia › Insecta › Diptera › Agromyzidae
Main crops: Common bean, Green bean, Cowpea, Mung bean, Soybean, Pigeon pea, Lima bean
Found in: Africa, South and South-East Asia, Oceania, Americas
Chemical groups: IRAC 4A, IRAC 28 (mode-of-action groups, not products)
Last reviewed: 2026-10-20

Bean fly scientific name, order and family

The scientific name of bean fly is Ophiomyia phaseoli Ophiomyia phaseoli (Tryon, 1895), in the order Diptera, family Agromyzidae.

Older or alternative scientific names: Agromyza phaseoli, Melanagromyza phaseoli.

Where it occurs

Found across Africa, South and South-East Asia, the Middle East, Australia and Pacific islands; not recorded in the Americas.

Region	Status
Africa	Widespread; major pest of common bean
South and South-East Asia	Widespread
Oceania	Present in Australia and Pacific islands
Americas	Not recorded

Symptoms and identification of bean fly

The organism

Adults are about 2 mm long, shiny black flies. Females make many tiny feeding and egg-laying punctures in leaves, which appear as pale spots. Maggots are small, pale and legless, and pupae are brown, barrel-shaped and found just under the skin at the base of the stem.

Signs in the crop, stage by stage

Crop stage	What you see
Leaves of seedlings	Many small pale spots (punctures) on the first leaves; short mines near the leaf stalk.
Stem base	Swollen, cracked stem at or just above the soil line; brown pupae visible under the skin when the stem is split.
Whole plant	Yellowing, stunting and wilting of young plants, which may die; surviving plants form new roots above the damaged area if soil covers it.

Life cycle of bean fly

Life cycle of Bean fly (bean stem maggot) — diagram drawn by Laisha from the stages below. Durations depend on temperature.

Females lay eggs inside the leaf tissue of seedlings. Each maggot mines into a leaf vein, down the leaf stalk and into the stem, where it feeds in the outer tissue at the base of the stem and then pupates under the skin. Adults emerge through a small window in the stem.

Stage	Duration	Notes
Egg (inside leaf)	About 2-4 days	Laid in young leaves.
Maggot (3 instars)	About 7-10 days	Mines down to the stem base.
Pupa (under stem skin)	About 7-10 days	Brown, barrel-shaped.
Adult fly	About 1-3 weeks	Active in the morning.

Temperature

One generation takes about three weeks in warm weather; populations build up when beans are planted continuously or in sequence.

Generations

Many generations per year where legumes are grown through the year.

Conditions that favour it

Late planting into high fly populations, poor soil fertility and dry soils that slow seedling growth, continuous or staggered bean planting, volunteer legumes and weeds, and lack of soil cover around the stem base.

Economic threshold level (ETL)

There is no single international threshold; because damage happens in the first weeks and is hidden inside the stem, management is mostly preventive in areas with a history of bean fly.

Thresholds are local. They depend on crop price, control cost, variety and natural-enemy activity, so use the figure your local extension service publishes where one exists.

Damage and yield loss from bean fly

Seedling deaths and stunting can reduce yields heavily on smallholder farms in Africa and Asia; losses are often reported between a third and all of the crop in bad years, especially in late or dry-season plantings.

Monitoring

Check the first leaves of seedlings for pale puncture marks within a week of emergence.
Split stems of wilting or yellowing seedlings at the base to look for maggots and pupae.
Note plant deaths over the first month to plan prevention for the next season.

How to control bean fly (integrated management)

Control works best as a sequence: prevent, monitor, then act only when a threshold or a risk forecast says so, using the least disruptive option that works.

Cultural control

Plant early in the rainy season and at the same time as neighbours, avoiding peaks of fly numbers.
Improve soil fertility with manure or fertiliser so that seedlings grow quickly, and ridge or hill up soil around the stem base so that damaged plants form new roots.
Mulch with crop residues; remove volunteer legumes and plough after harvest to destroy pupae in stubble.

Biological control

Parasitic wasps such as Opius phaseoli and other braconids and eulophids attack bean fly maggots and can be important where insecticides are not overused.

Host resistance

Some bean varieties tolerate attack by growing fast and producing new roots; tolerant and resistant lines have been identified in breeding programmes in Africa.

Chemical control of bean fly — by mode-of-action group only

Laisha names chemical options only by their resistance-committee mode-of-action group (IRAC for insects, mites and nematodes, FRAC for fungi, oomycetes and bacteria, HRAC for weeds), never by active ingredient or product. What is registered differs by country and changes over time; the label and your local plant-protection authority decide what may be used, on which crop, at what rate and with what pre-harvest interval.

Seed treatments protect seedlings during the first weeks and are the main chemical method on small farms. What is registered differs by country and changes over time; follow the label and your local plant-protection authority.

Scheme	Group	Mode of action	Notes
IRAC	4A	Nicotinic acetylcholine receptor competitive modulators (neonicotinoids), seed treatment	Toxic to pollinators and other non-targets.
IRAC	28	Ryanodine receptor modulators (diamides), seed treatment	Where registered.

Resistance management

Combine seed treatment with planting date, soil fertility and earthing up, and rotate groups between seasons.

Look-alikes and how to tell them apart

Serpentine leafminer — Long winding mines in leaves, without damage at the stem base.
Root rots of bean (Fusarium, Pythium, Rhizoctonia) — Rotten, discoloured roots and stem base without maggots or pupae under the skin.
Black cutworm — Seedlings cut through at the soil line by a caterpillar in the soil.

Host range

Common bean, runner and lima beans, cowpea, mung bean, black gram, soybean, pigeon pea and other cultivated and wild legumes.

What is still uncertain

The relative importance of the three Ophiomyia species differs between African regions.
Yield-loss figures vary widely between studies and seasons.

Grow guides for its host crops

How to grow the crop well is the first line of defence. Laisha's free grow guides cover each crop from sowing to harvest:

How to grow Common bean How to grow Green bean How to grow Cowpea How to grow Mung bean How to grow Soybean How to grow Pigeon pea How to grow Lima bean

Not sure this is what you are seeing?Ask Laisha: describe the symptoms or send a photo, and get a reasoned first read with what to check next — for your crop, your stage and your region.Ask Laisha

Sources

Ophiomyia phaseoli (bean fly) datasheet — CABI Compendium. https://doi.org/10.1079/cabicompendium.33002
The bean fly, Ophiomyia phaseoli (Tryon), and its parasitoids in Ethiopia — Journal of Applied Entomology (Wiley). https://doi.org/10.1111/j.1439-0418.1991.tb00324.x
Screening of common bean genotypes for their resistance to bean stem maggot (Ophiomyia spp.) in Ethiopia — Plant Protection. https://doi.org/10.33804/pp.008.01.4937
Postharvest tillage against bean fly in beans — PlantwisePlus Knowledge Bank (CABI). https://doi.org/10.1079/pwkb.20157800368

Written by Laisha from the sources above, in its own words. This page is general reference, not a prescription: confirm identification locally and follow the label and your plant-protection authority.