The National Accord association headed by Ali Selman and the National Democratic Act association said on Friday that a majority of their members had voted in favour of registering under the new law, despite its perceived shortcomings.
"We want our work to be legal, we can then better fight the disadvantages of this law," NDA president Ibrahim Sharif said.
The law was passed by parliament and ratified by King Hamad in July, after which a number of opposition groups said they were considering how to protest against the king's decision, one of which was "voluntarily closure".
At the time, the associations, which stand in place of banned political parties, said the law would restrict their funding by banning donations from foreign countries.
Opposition groups also objected to a provision raising the minimum age to join associations from 18 to 21.
The law states that political associations can be formed only so long as they are not based on class, profession, sectarian or geographical principles.
Bahrain allowed political groupings in 2001 to establish political associations. Several of these associations operate in the small Gulf kingdom representing Sunni and Shia Islamists, as well as liberals, leftists and Arab nationalists.