The move comes after a rare visit to North Korea by a senior UN official, who called for dialogue between Pyongyang and the international community to avert a potentially catastrophic "miscalculation" in the high-stakes nuclear crisis.
Seoul's new measures, its second set of unilateral sanctions in a month, are likely to draw an angry response from Pyongyang, which views its neighbour as overly-dependent on a hostile Washington.
"The organisations and individuals were involved in supplying money needed to develop weapons of mass destruction or illegal trading of sanctioned items," the official said, according to Yonhap.
The measures are in addition to those by the UN Security Council, which has hit the isolated and impoverished North with a package of sanctions over its increasingly powerful missile and nuclear tests.
China, Pyongyang's sole major diplomatic and military ally, has also backed the UN embargoes, but has repeatedly pushed for talks to diffuse tensions.
His trip also coincided with the US and South Korea's biggest-ever joint air exercise, which the North slammed as a provocation and revealing an intention to "mount a surprise nuclear pre-emptive strike".
Seoul's sanctions will bar South Korean individuals and entities from transacting with those on the list but it will be largely symbolic given a lack of inter-Korean economic ties.
Last year, South Korea unilaterally closed operations at the jointly-run Kaesong Industrial Complex, saying cash from the zone was being funnelled to the North's weapons programme.
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