The aim of our study was to understand the nalidixic acid resistance and clonal expansion of Salmonella enterica serotype Paratyphi A (SPA) recovered from patients with paratyphoid fever A in Yuxi City from 1999 to 2008. A typing method is needed to determine the epidemic clones of the isolates. Antimicrobial susceptibility testing was performed with 4 060 SPA isolates. 186 isolates were typed by pulsed-field gel electrophoresis (PFGE) with SpeI, and the MICs for nalidixic acid, ciprofloxacin, levofloxacin, ofloxacin, norfloxacin, and gatifloxacin were determined. The incidence of resistance to nalidixic acid of the isolates increased from 12.5% in 1999, 82.2% in 2000, 93.0% in 2001, to100% in 2008. Nalidixic acid-susceptible (NAS) isolates predominated in 1999 but was replaced by nalidixic acid-resistant (NAR) isolates after 2000. The frequencies of intermediary and susceptibility (Kirby-Bauer disc diffusion technique) to ciprofloxacin were 17.0% and 83.0% before 2005, 65.3% and 34.7% in 2008, respectively. A group of 166 NAR and 20 NAS isolates of SPA were randomly selected. SpeI digestion of 186 isolates gave nine different PFGE patterns with predominance of the SpeI01 and SpeI02 epidemic patterns. All NAR isolates studied had a reduced susceptibility to fluoroquinolone, the MICs were higher than that for 20 NAS isolates.We validate the use of the nalidixic acid screening test in the detection of decreased fluoroquinolone susceptibility in SPA. PFGE patterns SpeI01 and SpeI02, the main clones of the epidemics, are highly prevalent and NAR isolates in Yuxi. Recommendation for the emergency treatments of outbreaks and epidemics caused by a fully fluoroquinolone-resistant strain can be made. PFGE with SpeI is a useful technique to differentiate SPA.