Bacidina margallensis and B. iqbalii from Pakistan are described and illustrated. Phylogeny of ITS nrDNA region confirms their position within the genus Bacidina, and morphological data make them distinct from other known species of the genus. Based on molecular data, corticolous Bacidina margallensis appears to be a sister species to B. chloroticula, but morphologically, when dry, is the most similar to known from Europe B. mendax because of the granular and warted greenish grey thallus, whitish-cream to dark brown and often piebald apothecia. It differs from that species by shorter, wider and less septate ascospores; 1–3-septate in B. margallensis vs 3–5(6)-septate in B. mendax, and by unusual parrot-green colour of wet thallus. Saxicolous Bacidina iqbalii is closely related to B. neosquamulosa but differs in having crustaceous thallus, transculent when wet entirely pale apothecia, larger asci and less septate large ascospores.