Thomas will be contesting from Tura North constituency in West Garo Hills district while Shullai will be contesting from Shillong South, state party president W R Kharlukhi said.
The other candidates include that of Clement Momin who will take on Chief Minister Mukul Sangma from Ampati constituency in West Haro Hills district.
Kharlukhi maintained that the third list would be out within a month and after receiving inputs from the party observers in the constituencies.
The NCP leaders said the party is keen at contesting in all seats where there is a "strong chance of winning" factor.
The party intends to put up candidates in all 24 assemble seats in Garo Hills region, once considered to the the stronghold of the NCP.
In a house of 60, the NCP has 15 MLAs; 13 are elected from Garo Hills and 2 from the Khasi Jaintia Hills while one was suspended for indulging in "anti-party" activities.
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"Unlike the Congress, our goal is to announce our candidates early and we will go to work early," Opposition Leader Conrad K Sangma said, even as he dared the Congress to announce the list of candidates early.
The NCP had earlier released the list of 19 candidates which include that of Conrad who will be contesting from Selsella constituency.