Glyphosate-resistant (GR) kochia is an increasing concern for growers across the U.S. Great Plains and Canadian prairies. Integrated strategies to mitigate resistance will require an improved understanding of the seed germination dynamics of GR kochia populations. Experiments were conducted to characterize the germination of GR vs. glyphosate-susceptible (GS) kochia populations under different constant (5 to 35 C) and alternating (5/10 to 30/35 C) temperatures. Seven GR and two GS populations were collected from wheat–fallow fields in northern Montana. Selected lines of GR and GS were obtained after three generations of recurrent group selection in the greenhouse. The GR-selected lines had 4.1 to 10.8 average EPSPS copies compared with a single EPSPS gene copy for the GS selected lines. Four out of seven GR selected lines had lower final germination (d parameter) and took more time to complete 50% cumulative germination (I50 values) under all constant and alternating temperatures, compared with the GS selected lines. Those GR selected lines also had a delayed germination initiation (I10 values), particularly at lower temperatures (5 to 10 C constant or 5/10 C alternating). In contrast, the final germination (d) of the other three GR selected lines did not differ from GS lines at a majority of temperatures tested. The I50 values of those GR lines were also comparable to GS lines under a majority of the temperatures. There was no significant correlation of observed percent cumulative germination and EPSPS gene copy number of selected kochia lines. The temperature-dependent dormancy and altered germination characteristics of the four GR kochia lines reflect the common selection of resistance and avoidance (glyphosate or other preseeding treatments) mechanisms. This is most likely attributed to long-term, intensive cropping practices and less diverse weed control methods, rather than a fitness cost or pleiotropic effect of multiple copies of the EPSPS gene.