This study evaluated different gilt vaccination protocols against Mycoplasma (M.) hyopneumoniae at acclimation and their effect on the genetic diversity. A total of 180 M. hyopneumoniae naïve gilts were selected 1 week post-entry (wpe) at the acclimation barn in a clinically affected M. hyopneumoniae farm. Gilts were distributed according to the M. hyopneumoniae antibodies levels into three different vaccination schedules: A) four doses of a M. hyopneumoniae commercial vaccine at 2, 4, 6 and 8 wpe; B) two vaccine doses at 2 and 6 wpe and PBS at 4 and 8 wpe; and C) four PBS doses at the same wpe. Detection of M. hyopneumoniae (rt-PCR) and antibodies (ELISA) were assessed in gilts at 1, 14, 27 and 34 wpe and in 6 of their piglets at weaning. rt-PCR positive gilts were detected at 14 wpe, being the proportion significantly lower in groups A and B (3/120, 3%) than C (27/60, 45%). Seroconversion was detected at 14 wpe, showing significant differences in percentage of inhibition (PI) between groups A (median 4.9, range 3.1-19.9) and B (5.5, 3.7-13.5), and C (14.3, 3.3-53.2). Gilts remained seropositive over the study; significant differences in PI were detected between groups A and B versus C. Piglets were rt-PCR negative; proportion of seropositive piglets coming from vaccinated gilts was significantly higher than the non-vaccinated group. M. hyopneumoniae characterization showed high variability. Hence, gilt vaccination with 2 or 4 doses significantly decreased the pathogen infectious pressure, variability, and provided high antibody levels to gilts and their offspring.