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Salmonella enterica is a diverse bacterial pathogen consisting of both typhoidal and nontyphoidal clinically distinct serovars. While typhoidal serovars cause in humans a systemic life-threatening enteric fever, nontyphoidal Salmonella (NTS) usually provoke a localized self-limiting gastroenteritis. Factors responsible for the different diseases caused by distinct Salmonella serovars are still poorly understood. Here, we show that at elevated physiological temperature, manifested during enteric fever (39–40°C), the transcription of the flagellar regulon, its protein translation, and flagella-mediated motility are all repressed in the typhoidal serovar, S. Paratyphi A. In contrast, the NTS representative serovar, S. Typhimurium, maintains similar or even higher levels of flagellar genes transcription, translation, and motility at 40°C relative to 37°C. By using a temperature-responsive chromogenic reporter system in conjunction with a dense transposon mutagenesis screen we found that under elevated temperature, HilE negatively regulates S. Paratyphi A motility in a HilD-dependent manner. Because HilD is required for the transcriptional activation of flhDC, encoding the master regulator of the Salmonella flagellar-chemotaxis regulon, null deletion of hilE leads to motility upregulation at elevated temperature and the loss of motility thermoregulation in S. Paratyphi A. Moreover, we show that a HilE-mediated motility thermoregulation is common to other typhoidal serovars, including S. Typhi and S. Sendai, but not to S. Paratyphi B, nor to various NTS serovars. Interestingly, the absence of HilE also leads to a hyper-uptake of S. Paratyphi A by THP-1 human macrophages at 40°C, but not at 37°C. Based on these results, we propose that HilE plays a unique role in motility thermoregulation in typhoidal Salmonella in a way that may restrain systemic dissemination of the pathogen via professional phagocytes, during the acute phase of enteric fever.