Silver(I) complexes with aromatic nitrogen-containing heterocycles have shown an effective and wide-spectrum of antimicrobial activity. The possible mechanism of their antimicrobial activity can be attributed to interactions of these complexes with biomolecules, including DNA and proteins. Herein, we investigated the interactions of two antimicrobial active dinuclear phthalazine-silver(I) complexes, [{Ag(NO₃)(phtz)}₂(μ-phtz)₂] (Ag1) and [{Ag(CF₃SO₃)(phtz)}₂(μ-phtz)₂] (Ag2) (phtz is phthalazine), with calf thymus DNA (ctDNA) and bovine serum albumin (BSA) to evaluate their binding affinities towards these biomolecules for possible insights on their mode of antimicrobial activity. The value of binding constants (K_A) of Ag1 and Ag2 to BSA is higher than that for DNA, indicating greater affinity of the complexes toward this model protein. The partition coefficient (logP) values for Ag1 and Ag2 are 0.0035 and -0.0063, respectively, what is in accordance with higher cellular uptake efficiency and better antibacterial activity of Ag1 in respect to Ag2. In order to determine the therapeutic potential of Ag1 and Ag2 complexes, their toxicity in vivo against nematode, Caenorhabditis elegans, was investigated.