Vaquitas have probably always been rare.
Historical abundance of the vaquita is unknown, but genetic evidence indicates that the population was never large.
Judging by the results of simulations of plausible population dynamics, their loss of genomic variability likely occurred over evolutionary time. No polymorphism has been found in the mitochondrial DNA control region and in the DQB locus of the Major Histocompatibility Complex, (MHC,) and limited diversity was found in the DRB locus of the HMC, of 43, 25 and 29 vaquita specimens, respectively. These findings are consistent with the hypothesis that the evolutionary history of the species included a bottleneck or founder event and that its extreme loss of genomic variability occurred over evolutionary time rather than being caused by human activities.
Sources: (Mungia-Vega, Esquer-Garrigos, Rojas-Bracho, Vazquez-Juarez, Castro-Prieto, & Flores-Ramirez, 2007; Rojas-Bracho, Reeves, & Jaramillo-Legorreta, 2006; Rosel & Rojas-Bracho, 1999)