This dataset of atmospheric ozone (O3) has been generated from solar absorption spectra measured in central Mexico using ground-based Fourier-Transform Infrared (FTIR) spectrometers. The FTIR experiments have been operated by the “Spectroscopy and Remote Sensing” Research Group of the Centro de Ciencias de la Atmósfera of the Universidad Nacional Autónoma de México (http://www.atmosfera.unam.mx/espectroscopia/index.html). The dataset covers measurements made between November 2012 and February 2014 applying two different FTIR spectrometers. The first instrument offers very high resolution spectra and contributes to NDACC (Network for the Detection of Atmospheric Composition Change). It is located at the mountain observatory of Altzomoni (ALTZ) about 1700m above the Mexico City basin. The second instrument has a medium spectral resolution and is located inside of Mexico City at the Universidad Nacional Autónoma de México (UNAM) at a horizontal distance of about 60km to the mountain observatory. The here provided dataset consists of two NETCDF data-files for each station and a MATLAB script for reading the NETCDF files. The files “ALTZ_IFS125_O3.nc” and “UNAM_IFS125_O3.nc” contain the retrieved O3 state vectors, the O3 averaging kernels and the O3 a priori profiles, together with auxiliary data: observation time, observation geometry, instrumental settings, atmospheric temperature and humidity profiles. The data as well as the method for combining the two different observations are presented in Plaza-Medina et al. (2017), which should be consulted for more details. The files “ALTZ_IFS125_O3_Jac+Gain.nc” and “UNAM_IFS125_O3_Jac+Gain.nc” contain the Jacobians (for O3 as well as for error sources) and the Gain matrix, together with the auxiliary data. The MATLAB script “readNETCDF_and_combine2FTIR.m” reads the NETCDF files and performs the operations needed for the generation of a combined product, thereby exploiting the synergetic effects of two observations made in coincidence but at different ground altitudes. A related dataset with Altzomoni O3 profiles obtained by applying slightly different retrieval settings is available at the NDACC database (ftp://ftp.cpc.ncep.noaa.gov/ndacc/station/altzomoni/hdf/ftir/). Further datasets of atmospheric parameters as measured by different techniques are available at the webpage of the Red Universitario de Observaciones Atmosfericas (www.ruoa.unam.mx).