Electronic structure and thermoelectric properties of marcasite (m) and synthetic pyrite (p) phases of FeX2 (X = Se, Te) have been investigated using first principles density functional theory and Boltzmann transport equation. The plane wave pseudopotential approximation was used to study the structural properties and full-potential linear augmented plane wave method was used to obtain the electronic structure and thermoelectric properties (thermopower and power factor scaled by relaxation time). From total energy calculations we find that m-FeSe2 and m-FeTe2 are stable at ambient conditions and no structural transition from marcasite to pyrite is seen under the application of hydrostatic pressure. The calculated ground state structural properties agree quite well with available experiments. From the calculated thermoelectric properties, we find that both m and p forms are good candidates for thermoelectric applications. However, hole doped m-FeSe 2 appears to be the best among all the four systems. © 2014 The Royal Society of Chemistry.