Reports of novel emerging and resurging wildlife and zoonotic diseases have increased. Consequently, integration of pathogen sampling into wildlife monitoring programs has grown. Sampling frequency influences interpretations of coupled host-pathogen dynamics, with direct implication to human exposure risk, but has received little empirical attention. To address this, a 15-year study, based on monthly sampling, of deer mouse (Peromyscus maniculatus) populations and Sin Nombre virus (SNV; a virulent disease in humans) dynamics was evaluated. Estimates of deer mouse abundance, number infected with SNV, and SNV prevalence from sampling less frequently than each month (achieved by deletion of months and recalculation of these parameters) were compared to monthly sampling frequencies. Deer mouse abundance was underestimated (10%-20%), SNV prevalence was overestimated when prevalence was high (>15%), and fewer annual extremes of abundance and infection were detected when sampling frequency was less than monthly. Effort necessary to detect temporal dynamics of SNV differed from effort to detect demographic patterns in deer mouse abundance. Findings here are applicable to sampling strategies for other host-pathogen dynamics and have direct implications for allocation of public health resources and intervention programs.