For the second time, the moss biomonitoring technique was applied to evaluate the deposition of potentially toxic elements in the Republic of Moldova. The study was performed in the framework of the International Cooperative Program on Effects of Air Pollution on Natural Vegetation and Crops. Moss Hypnum cupressiforme Hedw. samples were collected in May 2020 from 41 sampling sites distributed over the entire territory of the country. The mass fractions of 35 elements (Na, Mg, Al, Cl, K, Ca, Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, As, Br, Se, Rb, Sr, Sb, Cs, Ba, Cd, La, Ce, Sm, Eu, Tb, Hf, Ta, Th, Pb, and U) were determined using neutron activation analysis and atomic absorption spectrometry. Comparing with 2015/2016 moss survey data, significant differences in the mass fractions of Cr, As, Se, Br, Sr, Sb, Cd, Pb, and Cu were found. Main air pollution sources (natural processes, transport, industry, agriculture, mining) were identified and characterized using factor and correlation analyses. GIS maps were built to point out the zones with the highest element mass fractions and to relate this to the known sources of contamination. Contamination factor, geo-accumulation index, pollution load index, and potential ecological risk index were calculated to assess the air pollution levels in the country. According to the calculated values, Moldova can be characterized as unpolluted to moderately polluted, with low potential ecological risk related to the degree of atmospheric deposition of potentially toxic elements. The cities of Chisinau and Balti were determined to experience particular environmental stress and are considered moderately polluted.