Lactobacillus johnsonii and Lactobacillus zeae are among the lactobacilli with probiotic properties, which occur in sour milk products, cheeses, and to a lesser extent in raw milk. Recently, resistant strains have been detected in various species of lactobacilli. The aim of the study was to determine the incidence of resistant Lactobacillus johnsonii and Lactobacillus zeae strains in various types of raw milk. A total of 245 isolates were identified by matrix-assisted laser desorption/ionization mass spectrometry and polymerase chain reaction methods as Lactobacillus sp., of which 23 isolates of Lactobacillus johnsonii and 18 isolates of Lactobacillus zeae were confirmed. Determination of susceptibility to selected antibiotics was performed using the E-test and broth dilution method, where 7.3% of lactobacilli strains were evaluated as ampicillin-resistant, 14.7% of isolates as erythromycin-resistant, and 4.9% of isolates as clindamycin-resistant. The genus Lactobacillus johnsonii had the highest resistance to erythromycin (34.8%), similar to Lactobacillus zeae (33.3%). Of the 41 isolates, the presence of the gene was confirmed in five Lactobacillus johnsonii strains and in two strains of Lactobacillus zeae. The presence of resistant strains of Lactobacillus johnsonii and Lactobacillus zeae is a potential risk in terms of spreading antimicrobial resistance through the food chain.