The 27-year-old Brigitte Garcia and her press officer were found dead in a car on Sunday in the town of San Vicente, where she had won the mayoral election last year, BBC reports.
No arrests have been made so far and it is not clear what the motive may be.
Ms Brigitte García is the latest politician to be killed in the Andean country, which last year was rocked by the assassination of presidential candidate Fernando Villavicencio.
The bodies of Ms Brigitte García and communications director Jairo Loor were found in the early hours of Sunday, local time.
Police said the shots which killed them had been fired from inside the car they had rented.
Ms García, a nurse, had been elected mayor of San Vicente for the opposition Citizens’ Revolution party last year at the age of 26.
San Vicente, the town she governed, is located in the province of Manabí.
The coastal region has been particularly badly hit by violence linked to drug gangs which smuggle cocaine to lucrative markets in the US and Europe.
Brigitte Garcia is not the first politician in Manabí to be killed.
In July, a gunman shot dead the mayor of the port city of Manta, Agustín Intriago, who had been recently re-elected.
And in February of 2023, mayoral candidate Omar Menéndez was murdered just hours before polls opened in the city of Puerto López.
The violence has not been confined to Manabí.
In August, presidential candidate Fernando Villavicencio was gunned down as he was leaving a campaign rally in the capital, Quito.
Prosecutors investigating Villavicencio’s murder said it had been planned from inside jail by members of the Los Lobos criminal gang.
The rise of such gangs led President Daniel Noboa in January to declare a two-month-long state of emergency to combat armed groups.
It was extended by another month on 7 March.
The government says the security forces have carried out more than 150,000 operations since the state of emergency was declared and detained more than 10,000 suspects.
However, critics of the government say Ms García’s murder shows that more needs to be done to guarantee the safety of elected officials.
Luisa González, who was defeated by Mr Noboa in the presidential election, wrote on X, formerly known as Twitter, that “nobody is safe in Ecuador”.