The current study described the isolation and molecular detection of Mycoplasma gallisepticum (Mg) and Mycoplasma synoviae from tracheal swabs of diseased birds showing signs of respiratory distress in selected commercial (layer and broiler) farms and from yolk and an open air of pens of vaccinated breeder flocks in Sudan. A number of 45 Mycoplasma isolates were recovered from chickens in Khartoum, Gezira, and Equatoria states in Sudan. Of these, eight Mg and three Ms isolates were identified using growth inhibition and rapid serum agglutination (RSA) tests. The conventional PCR technique was applied to amplify 140 bp and 720 bp DNA fragments for the Mg and Ms, respectively. This research confirmed vertical and horizontal transmission of Mg from breeder farms through detection of Mg in yolk of fertile eggs and an air of pens despite previous vaccination. PCR is considered a rapid, sensitive, and cheap method and it will improve the diagnosis of Mycoplasma in chickens.