Objectives Candida species has emerged as a potentially pathogenic fungus rather than benefit mucosal commensal in patients with pulmonary diseases. Therefore, our study was carried out to detect Candida species in sputum samples from patients with pulmonary diseases using conventional and molecular methods. Methods A total of 100 sputum samples obtained from patients with pulmonary symptoms such as chronic productive cough, shortness of breath, wheezing and fever were included in this study. Sputum samples were dispensed into three specimen parts; the first one was applicated for cultured on Sabouraud dextrose agar at 37°C for 48 h and then the purified colony of Candida underwent biochemical tests including API, Candida strips, and germ tube. The second part was undergone direct gram stain, while the third part was applicated for DNA extraction and then molecular diagnosis with PCR technique using specific primers. Results Culture result revealed 43 positive samples for Candida species out of 100 samples. Among these positive samples, 23 (53.5%) were positive for C. albicans in each of culture and germ tube. API 20 Candida found that (40) samples were positive for Candida species as, 23 (57.5%) represent Candida albicans, 8 (20.0%) Candida glabrata, 4 (10.0%) Candida parapslosis, 4(10.0%) Candida tropicalis and only one (2.5%) as Candida krusei. Molecular test revealed that forty one samples out of forty three culture isolates of Candida species were positive as follow twenty three (53.48%), belong Candida albicans, Nine (20.93%) belong Candida glabrata, Six (13.95%) Candida parapslosis, Four (9.30%) belong Candida tropicalis. Conclusion Candida albicans is highly prevalent among patients suffering from bronchopulmonary symptoms. The molecular and conventional methods gave concomitant results as detection tools for the diagnosis of such microorganisms. Keywords Candida albicans, phospholipase B gene, OMNIgene, API 20 AUX