Atmospheric deposition is of great importance for the sink of air pollutants to the environment, either from local sources as well as coming from long range transport. To further understand the combined impact of both long-range transport from South East Asia and local emission sources of pollutants, the characteristics of polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) in the ambient air of two background sites in Taiwan namely, Hengchun (coastal area) and Lulin (high mountain area), were simulated by regression of PM10 versus total-PCDD/F mass concentration, modeling of gas-particle partitioning, and simulations of both dry and wet deposition. The simulated PCDD/F concentrations at Hengchun, ranged between 0.0039–0.0106 and 0.0054–0.0138 pg WHO2005-TEQ m–3 for 2012 and 2013, respectively. For Lulin site, the PCDD/F concentrations ranged between 0.0016–0.0029 and 0.0016–0.0032 pg WHO2005-TEQ m–3 for 2012 and 2013, respectively. The WHO2005-TEQ ratios of PCDDs to PCDFs at both sites were less than unity, indicating that PCDF dominated the total toxicity. The results show that higher chlorinated PCDD/Fs primarily present in particulate phase for all seasons at both sampling sites especially in winter. Average dry deposition fluxes at Hengchun (57.1 pg WHO2005-TEQ m–2 month–1) were approximately 5.1 times higher than those at Lulin (11.2 pg WHO2005-TEQ m–2 month–1). The annual average dry deposition velocities were estimated to be 0.28 and 0.22 cm/s for Henchun and Lulin, respectively. For the whole period (2012–2013), the mean monthly wet deposition fluxes at Hengchun (averaged 11.7 pg WHO2005-TEQ m–2 month–1) were 1.44 times higher than that at Lulin (averaged 8.11 pg WHO2005-TEQ m–2 month–1). The calculated annual average total-PCDD/Fs-WHO2005-TEQ concentrations in the rain were 0.064 and 0.027 pg WHO2005-TEQ L–1 for Henchun and Lulin, respectively. The estimated annual average scavenging ratios of total-PCDD/Fs-WHO2005-TEQ were 8015 and 13450 for Henchun and Lulin, respectively. Similarly, for the entire study period (2012–2013), the average annual total (dry + wet) deposition flux of total PCDD/Fs-WHO2005-TEQ in the terms of pg WHO2005-TEQ m–2 year–1 at Hengchun (824.9) was 3.5 times higher than those in Lulin (232.0). On the basis of total PCDD/Fs-WHO2005-TEQ, the mean fraction contributed by dry deposition at Hengchun were 78.2% and 78.9% in 2012 and 2013, respectively, while at Lulin the average fraction contributed by dry deposition at Lulin were 56.5% and 69.1% in 2012 and 2013, respectively. Higher chlorinated congeners OCDD, OCDF, 1,2,3,4,6,7,8-HpCDF and 1,2,3,4,6,7,8-HpCDD dominated in terms of mass fractions of total PCDD/F deposition fluxes for all seasons at both sites. However on the basis of total PCDD/Fs-WHO2005-TEQ deposition fluxes, the most dominant congeners were 2,3,4,7,8-PeCDF, 1,2,3,7,8-PeCDD and 2,3,7,8-TeCDD during the whole sampling period at both sites. The results of this study provide useful information for both environmental impact assessment and control strategies of persistent organic compounds (POPs).