Abstract This paper analyses the floristic biodiversity of weed communities in the arable lands of the Istrian peninsula during a twelve year period (2005–2017). A total of 50 fields were surveyed for each sampling time using the seven-degree Braun-Blanquet cover abundance scale in the following agricultural categories: a) permanent crops (vineyards/olive groves), b) alfalfa fields, c) cereals, d) row crops and e) ruderal areas. The taxonomic identification was performed during the full development of vegetation, for cereals in June and July, and for the rest – in August and September. A total of 175 weed species were determined during both study periods with and families as the most abundant. Altogether, therophytes were dominant in both surveys, followed by hemycryptophytes and geophytes. Variations in species composition were visible in both study periods (2005 and 2017) as well as in the selected habitat types. Exclusive species were found in addition to those that were common for both surveys. Changes in species composition between 2005 and 2017 referred to the difference in row spacing in earlier period, and ruderal vs. agricultural habitats in the recent survey. The differences in phenological traits between the past and present surveys were greatest for germination season in permanent crops and row crops, flowering start for permanent crops, flowering period for ruderal area and weed height for permanent crops. Significant differences between the past and present survey for other plant traits did not occur.