A 24-month clinical study was carried out to evaluate and compare the retention rate, marginal integrity and caries preventing effects of a polyacid-modified resin composite based fissure sealant, Dyract Seal, to that of a resin based fluoride fissure sealant, Delton FS+. Fifty-three patients (27 female and 26 male), 7 to 10 years old, were included in the study. At baseline, a total of 192 permanent first molars were sealed with either fissure sealant (n = 96, each), using invasive technique. The sealed teeth were evaluated at post-operative 3, 6, 12 and 24 months with respect to evaluation parameters. The data were analyzed with the Chi-Square tests where alpha = 0.05. There were no statistically significant differences between fissure sealants as regards to retention and prevention of caries for all periods of the evaluation (p > 0.05). However, regarding marginal integrity of the sealants, Delton FS+ gave significantly better results than Dyract Seal for the 3-, 6- and 12-month evaluations, respectively (p < 0.05). In conclusion, the use of Dyract Seal on permanent molars with invasive technique was found to be clinically comparable to Delton FS+ for the 24-month evaluation period.