The biggest of the tremors measuring 4.2 on the richer scale struck the city of Kaki, Bushehr Province, at approximately 09:23 local time (0453 GMT).
The epicenter of the main aftershock was located in an area 51.5 in longitude and 28.3 in latitude.
An earthquake measuring 6.1 on the Richter scale jolted the town of Kaki in Bushehr province on Tuesday, killing at least 39 people and injuring more than 750 others.
The Seismological center of Bushehr province affiliated to the Geophysics Institute of Tehran University registered the quake at 16:22 hours local time (1152 GMT).
The epicenter of the quake was located in an area 51.5 degrees in longitude and 28.4 degrees in latitude.
Iran sits astride several major faults in the earth's crust, and is prone to frequent earthquakes, many of which have been devastating.
The worst in recent times hit Bam in southeastern Kerman province in December 2003, killing 31,000 people - about a quarter of its population - and destroying the city's ancient mud-built citadel.
The deadliest quake in the country was in June 1990 and measured 7.7 on the Richter scale. About 37,000 people were killed and more than 100,000 injured in the northwestern provinces of Gilan and Zanjan. It devastated 27 towns and about 1,870 villages.