We analyse the carbon monoxide (CO), ethane (C2H6) and hydrogen cyanide (HCN) partial columns (from the ground to 12 km) derived from measurements by ground-based solar Fourier Transform Spectroscopy at Lauder, New Zealand (45° S, 170° E), and at Arrival Heights, Antarctica (78° S, 167° E), from 1997 to 2009. Significant negative trends are calculated for all species at both locations, based on the daily-mean observed time series, namely CO (−0.94 ± 0.47% yr−1), C2H6 (−2.37 ± 1.18% yr−1) and HCN (−0.93 ± 0.47% yr−1) at Lauder and CO (−0.92 ± 0.46% yr−1), C2H6 (−2.82 ± 1.37% yr−1) and HCN (−1.41 ± 0.71% yr−1) at Arrival Heights. The uncertainties reflect the 95% confidence limits. However, the magnitudes of the trends are influenced by the anomaly associated with the 1997–1998 El Niño Southern Oscillation event at the beginning of the time series reported. We calculate trends for each month from 1997 to 2009 and find negative trends for all months. The largest monthly trends of CO and C2H6 at Lauder, and to a lesser degree at Arrival Heights, occur during austral spring during the Southern Hemisphere tropical and subtropical biomass burning period. For HCN, the largest monthly trends occur in July and August at Lauder and around November at Arrival Heights. The correlations between CO and C2H6 and between CO and HCN at Lauder in September to November, when the biomass burning maximizes, are significantly larger that those in other seasons. A tropospheric chemistry-climate model is used to simulate CO, C2H6, and HCN partial columns for the period of 1997–2009, using interannually varying biomass burning emissions from GFED3 and annually periodic but seasonally varying emissions from both biogenic and anthropogenic sources. The model-simulated partial columns of these species compare well with the measured partial columns and the model accurately reproduces seasonal cycles of all three species at both locations. However, while the model satisfactorily captures both the seasonality and trends in HCN, it is not able to reproduce the negative trends in either C2H6 or CO. A further simulation assuming a 35% decline of C2H6 and a 26% decline of CO emissions from the industrial sources from 1997 to 2009 largely captures the observed trends of C2H6 and CO partial columns at both locations. Here we attribute trends in HCN exclusively to changes in biomass burning and thereby isolate the influence of anthropogenic emissions as responsible for the long-term decline in CO and C2H6. This analysis shows that biomass burning emissions are the main factors in controlling the interannual and seasonal variations of these species. We also demonstrate contributions of biomass burning emission from different southern tropical and sub-tropical regions to seasonal and interannual variations of CO at Lauder; it shows that long-range transport of biomass burning emissions from southern Africa and South America have consistently larger year-to-year contributions to the background seasonality of CO at Lauder than those from other regions (e.g. Australia and South-East Asia). However, large interannual anomalies are triggered by variations in biomass burning emissions associated with large-scale El Niño Southern Oscillation and prolonged biomass burning events, e.g. the Australian bush fires.