Booth founded Manor from his own double garage in Rotherham in 1990, while Lowdon was pivotal in keeping the cash-strapped team in business after they were entered into administration last year.
But both men are said to have grown frustrated with British businessman and team owner Stephen Fitzpatrick, and will leave their posts at the end of the season.
A team spokesman refused to comment on the reports in Mexico yesterday.
Manor began their journey in the sport in 2010 as Virgin Racing backed by British billionaire Sir Richard Branson, before being renamed Marussia.
The team scored their only-ever points at last year’s Monaco Grand Prix when Jules Bianchi, the Frenchman who suffered an ultimately fatal crash in Japan, finished ninth.
Russian Andrey Cheglakov ended his association with the team at the end of last year to leave the British-based outfit on the verge of extinction.
But Fitzpatrick poured in a reported £30m of his own money to rescue the team, which now compete under the guise of Manor. Former Sainsbury’s executive Justin King also joined as interim chairman.
Manor have competed at the back of the field this term, but are expected to be more competitive next season after agreeing a deal with Mercedes to use their engines from 2016 onwards.
The team are yet to announce their driver line-up for next season, but Englishman Will Stevens is hopeful of retaining his seat.
Speaking on Thursday ahead of the Mexican Grand Prix, Stevens, 25, said: “If I was to assess the year as a whole, I think it’s been really positive and for my options for next year, obviously we are pushing hard and everything is moving in the right direction.”
Max Verstappen finished a Formula One practice session on top of the timesheets for the first time in his career on Friday.
The 18-year-old Toro Rosso driver posted a best lap of one minute and 25.990 seconds to finish ahead of the field.