The aim of the study was to compare the prevalence of the nasopharyngeal carriage of culturable microorganisms in the microbiota of asymptomatic women with a physiological pregnancy (PW) and nonpregnant women (NPW). Nasopharyngeal swabs were collected from 53 PW and 30 NPW to detect bacterial and fungal colonization. Isolates were identified using the culture method and the MALDI-TOF MS technique. The nasopharyngeal microbiota (NPM) partially differed between PW and NPW. These differences in the frequency of nasopharyngeal colonization between the PW and NPW groups were not statistically significant (p> 0.05); all cases were colonized by bacteria and only two cases in the PW group were colonized by yeasts, namely,Rhodotorulaspp. High levels of staphylococcal colonization, including predominantly coagulase-negative staphylococci andS. aureusin the nasopharyngeal sample, were present in both groups. The reduced number of Gram-negative rods colonized in the cases studied was seen in samples from the NPW group, particularly withEnterobacterales, and anaerobicCutibacteriumspp. were isolated only in the PW group (p< 0.05). Moreover, a higher carriage rate ofEnterobacter aerogenescolonization was statistically significant (p< 0.05) and correlated with the NPW group. Pregnancy may disturb the composition of the NPM represented by commensals and opportunistic bacteria and promote yeast colonization as compared to nonpregnant women.