The aim of this study was to evaluate the effect of organic Se from Se-enriched alga (Chlorella spp.) and Se from Se-enriched yeast on concentrations of Se in serum and tissues, and serum GSH-Px activities and carcass characteristics in finishing pigs. The pigs were on experimental diets for a period of 3 months before slaughter with different Se supplements at the concentration of 0.3 mg Se per kg of feed. In group I (n = 12) the feed was supplemented with inorganic sodium selenite; in group II (n = 12) with organic Se from Se-enriched yeast; in group III (n = 12) with organic Se from Se-enriched alga, Chlorella spp. and pigs in group IV (n = 11) received a non-supplemented basal diet. The organic Se sources did not differ in serum Se and serum GSH-Px activities. Significantly higher Se concentrations in muscle (P < 0.01) and in the heart (P < 0.01) were found when Se from Se-enriched yeast was given, compared to the group of pigs that received Se from Se-enriched alga Chlorella spp. The Se content in livers and ovaries did not differ between the two organic Se sources. The use of both organic Se forms resulted in a higher accumulation in muscle tissue compared to the inorganic Se form. No differences in meat quality characteristics were found among the experimental groups. It is concluded that Se from Se-enriched alga, Chlorella spp. had a lower accumulation in muscle tissue than Se from Se-enriched yeast, and it did not affect meat quality.