The incident occurred on Tower Bridge at 10.38am this morning (April 27).
According to the Metropolitan Police, the protestors are linked to Youth Demand.
A member of London Marathon staff who was stationed on the bridge intervened to remove the protestors from the path of approaching male runners.
The pair were then arrested by Metropolitan Police officers on suspicion of causing a public nuisance, and they remain in custody at this time.
The paint thrown on the bridge appears to be chalk-based and is understood not to be a hazard to runners participating in the marathon.
A Met Police spokesperson said: “At around 10:38hrs, two protesters from Youth Demand jumped over barriers at Tower Bridge and threw red paint onto the road.
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“A member of London Marathon event staff intervened to remove the protesters from the path of the men’s elite race which was able to pass unobstructed moments later.
“He was quickly supported by police officers who arrested the protesters on suspicion of causing a public nuisance. They remain in custody.
“The paint appears to be chalk-based and is not expected to present a hazard to runners yet to pass this point.”