Citrus black spot (CBS), caused by Guignardia citricarpa, is an emerging disease in Florida. Fungicide applications are the main control measure worldwide. The in vitro activity and baseline sensitivity of G. citricarpa isolates to quinone outside inhibitor (QoI) fungicides (azoxystrobin and pyraclostrobin) were evaluated. The effective concentration needed to reduce mycelial growth or spore germination by 50% (EC50) was determined for 86 isolates obtained from Florida counties where CBS is found. The effect of salicylhydroxamic acid (SHAM) plus azoxystrobin and pyraclostrobin was also assessed for mycelial growth and conidial germination. The mean EC50 for mycelial growth for azoxystrobin was 0.027 μg/ml and that for pyraclostrobin was significantly lower at 0.007 μg/ml (P < 0.0001). Similarly, the mean EC50 for conidial germination for azoxystrobin was 0.016 μg/ml and that for pyraclostrobin was significantly lower at 0.008 μg/ml (P < 0.0001). There was no effect of SHAM on inhibition of mycelial growth or conidial germination by the QoI fungicides but SHAM slightly affected mycelium inhibition by pyraclostrobin. Cytochrome b was partially sequenced and three group 1 introns were found. One intron was immediately post G143, likely inhibiting resistance-conferring mutations at that site. It is surmised that the QoI resistance risk is low in the Florida G. citricarpa population.