Ruben Oseguera Gonzalez was captured in a dawn raid near Guadalajara - the capital of the western Jalisco state.
He is suspected to be second-in-command in the Jalisco New Generation cartel, led by his father Nemesio.
The gang is blamed for killing at least 20 police officers in March-April and May's shooting down of an army helicopter in which 10 people died.
Mr Oseguera Gonzalez, known as El Menchito, was arrested in Zapopan, near Guadalajara, the authorities said. No shots were fired.
This is the second time that he has been captured.
He was arrested in January 2014, but was released later that year for lack of evidence.
Mr Oseguera Gonzalez is suspected of controlling the cartel's finances and of buying drugs from South American countries.
The Jalisco New Generation cartel is involved in large-scale drug trafficking along Mexico's Pacific Coast.
It has recently increased its presence in the area, with Jalisco and the neighbouring Michoacan among Mexico's most violent states.
The Jalisco New Generation is also engaged in a turf war with the Knights Templar cartel.
Tens of thousands of people have been killed in drug-related violence in Mexico over the past eight years.

A number of houses were broken into early on Monday, officers said.
Goods left outside affected homes in the Calderdale of West Yorkshire were also stolen, it emerged.
"It is impossible to comprehend why anyone would want to bring further suffering to those already in a very vulnerable situation," said acting Supt Mark Grange, of North Yorkshire Police.
Houses in Huntingdon Road, York, were targeted after the River Foss broke its banks, with one being looted after the back door was forced, as well as tools being taken from a shed at another property.
West Yorkshire Police said it had received reports of people using white vans to take "dry goods left outside flooded homes", in the Calderdale area.
No arrests have been made in connection with the thefts and burglaries, which emerged after the levels of the Foss dropped by several metres on Tuesday.
Six severe flood warnings, in place since Boxing Day, were lifted by the Environment Agency, which said emergency repairs to the Foss Barrier had allowed four of eight pumps to begin working again.
Areas across northern England however, are braced for further disruption as Storm Frank, which hit the UK late on Tuesday, brings in more high winds and heavy rain.

Ann Khoshbin, owner of Rose Garden Day Nursery in Uplands, is to be awarded a British Empire Medal (BEM) for services to education.
She set up her business after being unable to find suitable childcare for her own children.
She said: "It's lovely, I'm pleased and humbled really.
She said of receiving the letter informing her of the honour: "It was such a surprise, I just cried, I couldn't believe it.
"I don't do the work to have a medal. I do it because I absolutely love it. It's a family business."
Mrs Khoshbin also provides work placements for college students and gives talks to students.
Unlike other honours, the BEM is not awarded by the Queen or Prince of Wales but by Lord-Lieutenants, who are the representatives of the Crown for each county in the UK.
Other recipients of BEMs from south-west Wales are:
Also recognised in the birthday honours list is Swansea councillor Peter Black who will be appointed CBE for services to politics and public life in Wales.
Mr Black was a Liberal Democrat AM between 1999 and 2016 and has represented the Cwmbwrla ward as a councillor since 1984.
British honours are awarded on merit, for exceptional achievement or service.
All of the recipients will be invited to a Buckingham Palace garden party to celebrate their achievements.
The Mexican authorities say they have arrested the son of one of the country's most wanted drug lords.
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Looters who targeted flood victims' homes in York have been condemned by police.
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The owner of a Swansea nursery has said she is "pleased and humbled" to be recognised in the Queen's birthday honours list.