The two markets were shut down for flouting the state's environmental laws.
The Lagos State government has sealed off Alaba Rago Market in Ojo and Alade Market in Ikeja for various environmental infractions.
The state governor's media aide, Jubril Gawat, made this known on Wednesday via his X account.
He said that the markers were sealed off for "lack of waste bin, filthy environment, illegal burning of refuse by the roadside. indiscriminate dumping of refuse.
"And failure to comply with the rules of Lagos State Waste Management Authority (LAWMA)."
According to the statement, the commissioner for Environment and Water Resources, Tokunbo Wahab, said the joint enforcement action by officials of the Lagos Waste Management Authority (LAWMA) and the Lagos State Environmental Sanitation Corps (LAGESC), was part of ongoing measures to sanitise markets.